Query 042463
Match_columns 490
No_of_seqs 308 out of 2814
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 06:26:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042463.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042463hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0564 RluA Pseudouridylate s 100.0 5.5E-56 1.2E-60 445.5 27.7 278 103-476 10-289 (289)
2 PRK11025 23S rRNA pseudouridyl 100.0 9E-55 1.9E-59 443.8 30.7 298 103-486 17-314 (317)
3 TIGR00005 rluA_subfam pseudour 100.0 1.1E-52 2.5E-57 425.1 28.9 294 103-485 3-298 (299)
4 PRK11180 rluD 23S rRNA pseudou 100.0 1.7E-52 3.6E-57 428.5 29.5 299 103-488 15-315 (325)
5 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 4.8E-46 1E-50 366.8 22.7 236 154-475 9-245 (246)
6 PRK11112 tRNA pseudouridine sy 100.0 5.3E-46 1.1E-50 368.7 21.2 224 204-487 3-236 (257)
7 cd02563 PseudoU_synth_TruC tRN 100.0 7.7E-45 1.7E-49 353.3 20.7 212 204-475 2-223 (223)
8 TIGR01621 RluA-like pseudourid 100.0 2.8E-44 6E-49 347.9 20.7 199 204-480 3-201 (217)
9 PRK10158 23S rRNA/tRNA pseudou 100.0 3.3E-44 7.2E-49 347.9 21.1 204 204-475 15-218 (219)
10 cd02557 PseudoU_synth_ScRIB2 P 100.0 1.9E-43 4.1E-48 341.3 19.3 194 204-478 17-212 (213)
11 KOG1919 RNA pseudouridylate sy 100.0 1.4E-37 3.1E-42 318.5 23.4 308 101-486 39-353 (371)
12 cd02869 PseudoU_synth_RluCD_li 100.0 1.4E-36 2.9E-41 285.6 18.1 164 212-399 1-166 (185)
13 PRK10839 16S rRNA pseudouridyl 100.0 8.1E-36 1.8E-40 291.6 14.9 200 106-394 1-201 (232)
14 PRK10475 23S rRNA pseudouridin 100.0 1.9E-31 4E-36 267.9 18.0 199 104-393 5-203 (290)
15 PRK10700 23S rRNA pseudouridyl 100.0 4.9E-31 1.1E-35 265.4 19.3 205 106-393 3-210 (289)
16 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 1.3E-30 2.7E-35 239.5 14.9 148 212-392 1-148 (154)
17 COG1187 RsuA 16S rRNA uridine- 100.0 5.5E-30 1.2E-34 249.9 15.8 206 105-394 2-211 (248)
18 PF00849 PseudoU_synth_2: RNA 100.0 2.3E-29 5E-34 232.2 15.6 153 211-383 1-163 (164)
19 cd02553 PseudoU_synth_RsuA Pse 100.0 4.1E-29 8.8E-34 232.6 11.1 144 212-398 2-145 (167)
20 cd02556 PseudoU_synth_RluB Pse 100.0 1.4E-28 3E-33 229.1 12.1 141 212-393 2-143 (167)
21 cd02870 PseudoU_synth_RsuA_lik 100.0 5.7E-29 1.2E-33 226.6 8.5 139 212-392 1-140 (146)
22 cd02566 PseudoU_synth_RluE Pse 99.9 6.8E-27 1.5E-31 217.9 10.5 154 212-396 1-158 (168)
23 PRK11394 23S rRNA pseudouridin 99.9 1E-25 2.3E-30 216.8 11.1 156 210-398 39-199 (217)
24 cd02555 PSSA_1 PSSA_1: Pseudou 99.9 1.4E-25 3E-30 210.6 10.8 142 211-397 5-154 (177)
25 TIGR00093 pseudouridine syntha 99.9 3.9E-24 8.5E-29 190.6 8.1 109 252-397 1-109 (128)
26 cd02554 PseudoU_synth_RluF Pse 99.9 3E-23 6.4E-28 192.3 11.5 136 212-394 2-137 (164)
27 cd02868 PseudoU_synth_hTruB2_l 98.8 7.6E-09 1.6E-13 100.7 7.8 73 212-307 2-75 (226)
28 cd00165 S4 S4/Hsp/ tRNA synthe 98.7 6.8E-08 1.5E-12 74.8 7.8 69 106-216 1-70 (70)
29 PF01479 S4: S4 domain; Inter 98.3 2E-06 4.4E-11 63.1 5.7 48 106-168 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 98.1 6.4E-06 1.4E-10 63.4 5.8 51 104-170 7-58 (59)
31 COG1188 Ribosome-associated he 97.6 9.8E-05 2.1E-09 62.4 5.1 56 103-174 6-61 (100)
32 cd02572 PseudoU_synth_hDyskeri 97.6 0.00023 5E-09 67.3 7.7 70 210-308 2-71 (182)
33 smart00363 S4 S4 RNA-binding d 97.4 0.00037 8.1E-09 51.9 6.2 51 106-172 1-52 (60)
34 PRK00989 truB tRNA pseudouridi 97.3 0.00052 1.1E-08 67.0 7.0 70 211-308 10-79 (230)
35 cd00506 PseudoU_synth_TruB_lik 97.2 0.00094 2E-08 64.6 7.3 68 212-308 2-69 (210)
36 PRK10348 ribosome-associated h 97.2 0.00085 1.8E-08 60.1 6.4 53 104-172 7-59 (133)
37 TIGR00431 TruB tRNA pseudourid 97.2 0.001 2.2E-08 64.2 7.5 69 211-308 3-71 (209)
38 PRK00020 truB tRNA pseudouridi 97.2 0.0012 2.6E-08 65.0 7.8 70 210-308 10-79 (244)
39 PRK04099 truB tRNA pseudouridi 97.2 0.0011 2.4E-08 66.3 7.6 70 210-308 2-71 (273)
40 PRK02484 truB tRNA pseudouridi 97.0 0.0018 3.8E-08 65.7 7.8 69 211-308 4-72 (294)
41 PRK02193 truB tRNA pseudouridi 97.0 0.0019 4.1E-08 65.0 7.4 68 212-308 2-69 (279)
42 PRK14123 tRNA pseudouridine sy 97.0 0.0021 4.5E-08 65.5 7.8 69 211-308 4-72 (305)
43 PRK00130 truB tRNA pseudouridi 97.0 0.0024 5.2E-08 64.7 7.9 70 210-308 2-71 (290)
44 PRK14846 truB tRNA pseudouridi 97.0 0.0023 4.9E-08 65.7 7.8 70 210-308 3-72 (345)
45 PRK03287 truB tRNA pseudouridi 96.9 0.0022 4.8E-08 65.1 7.5 70 210-308 9-78 (298)
46 PRK05389 truB tRNA pseudouridi 96.9 0.0025 5.4E-08 65.0 7.6 70 210-308 13-82 (305)
47 PRK14124 tRNA pseudouridine sy 96.9 0.0029 6.3E-08 64.5 8.0 70 210-308 3-72 (308)
48 PRK04270 H/ACA RNA-protein com 96.9 0.0023 5.1E-08 65.2 7.4 73 207-308 19-91 (300)
49 PRK01550 truB tRNA pseudouridi 96.9 0.003 6.5E-08 64.4 7.9 70 210-308 2-71 (304)
50 PLN00051 RNA-binding S4 domain 96.9 0.0015 3.2E-08 65.5 5.7 53 104-172 190-242 (267)
51 cd02573 PseudoU_synth_EcTruB P 96.9 0.0028 6.1E-08 63.8 7.6 68 212-308 2-69 (277)
52 PRK01851 truB tRNA pseudouridi 96.9 0.0032 6.9E-08 64.0 7.9 70 210-308 16-85 (303)
53 PRK05033 truB tRNA pseudouridi 96.9 0.0032 6.9E-08 64.3 7.9 70 210-308 10-79 (312)
54 PRK01528 truB tRNA pseudouridi 96.8 0.0035 7.5E-08 63.5 7.8 70 210-308 3-72 (292)
55 PRK14122 tRNA pseudouridine sy 96.7 0.0041 8.8E-08 63.5 7.4 68 212-308 3-70 (312)
56 TIGR01017 rpsD_bact ribosomal 96.7 0.0029 6.3E-08 60.8 5.7 54 105-173 89-142 (200)
57 PRK02755 truB tRNA pseudouridi 96.7 0.005 1.1E-07 62.5 7.7 69 210-308 3-71 (295)
58 TIGR03069 PS_II_S4 photosystem 96.6 0.0026 5.7E-08 63.4 5.3 54 103-172 181-234 (257)
59 CHL00113 rps4 ribosomal protei 96.6 0.0037 8.1E-08 60.0 5.7 54 105-173 88-141 (201)
60 PRK04642 truB tRNA pseudouridi 96.4 0.0085 1.8E-07 60.9 7.6 70 210-308 10-79 (300)
61 TIGR00425 CBF5 rRNA pseudourid 96.4 0.0069 1.5E-07 62.4 6.9 71 209-308 33-103 (322)
62 TIGR00478 tly hemolysin TlyA f 96.3 0.0061 1.3E-07 59.8 5.3 51 107-172 1-51 (228)
63 cd01291 PseudoU_synth PseudoU_ 96.2 0.022 4.8E-07 47.0 7.5 22 245-266 22-43 (87)
64 PRK05327 rpsD 30S ribosomal pr 96.1 0.0099 2.1E-07 57.3 5.5 53 105-172 92-144 (203)
65 COG0130 TruB Pseudouridine syn 96.1 0.015 3.2E-07 58.4 6.8 69 211-308 16-84 (271)
66 COG2302 Uncharacterized conser 95.5 0.014 3.1E-07 57.2 4.2 52 105-172 180-231 (257)
67 cd02867 PseudoU_synth_TruB_4 P 95.5 0.037 8E-07 56.6 7.1 43 247-308 56-98 (312)
68 PRK11507 ribosome-associated p 95.0 0.063 1.4E-06 42.8 5.5 54 104-172 10-63 (70)
69 COG1189 Predicted rRNA methyla 94.5 0.064 1.4E-06 52.6 5.4 52 105-171 2-53 (245)
70 COG2501 S4-like RNA binding pr 92.5 0.3 6.5E-06 39.2 5.3 55 103-172 9-63 (73)
71 COG0522 RpsD Ribosomal protein 92.1 0.22 4.9E-06 48.0 4.9 51 107-172 95-145 (205)
72 PF13275 S4_2: S4 domain; PDB: 91.9 0.046 1E-06 42.9 -0.1 53 104-171 6-58 (65)
73 PRK04051 rps4p 30S ribosomal p 87.1 0.99 2.1E-05 42.6 4.8 51 105-170 102-154 (177)
74 PRK04313 30S ribosomal protein 80.0 7.5 0.00016 38.4 7.8 54 103-171 35-89 (237)
75 PTZ00223 40S ribosomal protein 76.3 12 0.00025 37.8 8.0 54 103-171 36-90 (273)
76 PLN00036 40S ribosomal protein 75.9 13 0.00027 37.3 8.1 54 103-171 39-93 (261)
77 PTZ00118 40S ribosomal protein 74.5 14 0.0003 37.0 8.0 54 103-171 39-93 (262)
78 PF06353 DUF1062: Protein of u 74.3 4.6 0.0001 36.8 4.3 33 103-136 100-132 (142)
79 PF01509 TruB_N: TruB family p 71.4 3.4 7.5E-05 37.9 2.8 44 246-308 6-49 (149)
80 TIGR01018 rpsD_arch ribosomal 69.2 7.5 0.00016 36.2 4.5 49 107-170 105-155 (162)
81 COG4332 Uncharacterized protei 65.8 7 0.00015 36.8 3.5 34 102-136 135-168 (203)
82 KOG0062 ATPase component of AB 64.1 13 0.00028 40.7 5.7 101 105-274 443-544 (582)
83 COG1471 RPS4A Ribosomal protei 63.8 26 0.00055 34.5 7.1 49 106-171 41-92 (241)
84 PLN00189 40S ribosomal protein 63.3 4.4 9.5E-05 38.7 1.8 53 105-172 100-160 (194)
85 PRK01777 hypothetical protein; 54.6 16 0.00034 30.9 3.5 53 102-172 23-75 (95)
86 PTZ00155 40S ribosomal protein 50.1 13 0.00029 35.2 2.6 38 118-170 119-156 (181)
87 PF14451 Ub-Mut7C: Mut7-C ubiq 44.4 22 0.00047 29.2 2.8 46 103-172 30-75 (81)
88 KOG2559 Predicted pseudouridin 41.0 13 0.00029 36.6 1.2 22 248-269 90-111 (318)
89 PRK13354 tyrosyl-tRNA syntheta 40.4 36 0.00078 36.5 4.4 32 105-136 342-373 (410)
90 cd00754 MoaD Ubiquitin domain 38.6 59 0.0013 25.6 4.5 46 105-170 25-73 (80)
91 PRK05912 tyrosyl-tRNA syntheta 37.6 67 0.0015 34.3 5.9 32 105-136 342-373 (408)
92 PRK08364 sulfur carrier protei 28.8 1.2E+02 0.0026 23.8 4.6 42 104-170 22-63 (70)
93 KOG2529 Pseudouridine synthase 23.5 93 0.002 33.0 4.0 77 207-312 65-141 (395)
94 PRK11130 moaD molybdopterin sy 23.3 1.8E+02 0.0038 23.4 4.8 44 107-171 30-75 (81)
95 PRK05659 sulfur carrier protei 20.8 91 0.002 23.8 2.5 47 103-170 13-59 (66)
96 PF08068 DKCLD: DKCLD (NUC011) 20.6 50 0.0011 25.5 1.0 18 207-224 39-56 (59)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-56 Score=445.54 Aligned_cols=278 Identities=30% Similarity=0.438 Sum_probs=217.9
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR 182 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~ 182 (490)
..++|+++||+..++ +||+.++++|++|+|+|| |+ +++.++++..||+|.+........
T Consensus 10 ~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vN-----------g~-----~v~~~~~l~~gd~i~~~~~~~~~~---- 68 (289)
T COG0564 10 EAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVN-----------GK-----KVKPSYKLKPGDVVRIPLPEEPEE---- 68 (289)
T ss_pred hcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEEC-----------CE-----EccCCeeeCCCCEEEEeccccccc----
Confidence 357899999999666 999999999999999999 73 666999999999999966432210
Q ss_pred ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccC--CCCCccccCCCcCCc
Q 042463 183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDY--NEGPKLVHRLDRESS 260 (490)
Q Consensus 183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~--~~~l~~VHRLDr~TS 260 (490)
. .+.+.++ ...|||||+++||||||+||+||++. .+. ..+++..++.... ..++++||||||+||
T Consensus 69 ------~--~~~~~~~---~l~IlyED~~llVvnKP~Gl~vhp~~-~~~-~~tl~~~l~~~~~~~~~~~~~vHRLDkdTS 135 (289)
T COG0564 69 ------E--KLVPEDI---PLDILYEDEDLLVVNKPAGLVVHPGG-GHH-EGTLVNALLRHCQDGVERPGIVHRLDKDTS 135 (289)
T ss_pred ------c--cccccCC---CccEEEecCCEEEEECCCCCcCcCCC-CCc-cHhHHHHHHHhccccCCceeeeccCCCCCc
Confidence 0 0111111 13599999999999999999999873 332 2455554443322 567999999999999
Q ss_pred eeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeec
Q 042463 261 GLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQN 340 (490)
Q Consensus 261 GLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~ 340 (490)
||||+|||..++..|+.+|+++ .+.|+|+|+|.|.++..+|.|+.||.+...... .+.+...
T Consensus 136 Glll~AK~~~a~~~l~~~f~~r---------------~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~--~~~v~~~- 197 (289)
T COG0564 136 GLLLVAKNREAARELSEQFKQR---------------KVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRK--KMAVVKE- 197 (289)
T ss_pred eEEEEECCHHHHHHHHHHHhcC---------------cCcEEEEEEEECcccCCCCEEeeeeecCCcCCc--eEEEecc-
Confidence 9999999999999999999997 599999999999999888999999988643322 2222211
Q ss_pred CCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCce
Q 042463 341 SGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPY 420 (490)
Q Consensus 341 ~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~ 420 (490)
..++.|+|+|++++...+..||++|+|+||||||||+||+ ++||||+||.+||... .
T Consensus 198 ---~~gk~A~T~~~~l~~~~~~~tlv~~~~~TGRTHQIRVHl~-~lghPI~GD~~Yg~~~--~----------------- 254 (289)
T COG0564 198 ---GSGKPAITHYEVLERFGDNYTLVELKPETGRTHQIRVHLA-HLGHPIVGDPLYGGKD--K----------------- 254 (289)
T ss_pred ---CCCCceEEEEEehhccCCceEEEEEEeCCCCHhHHHHHHH-HCCCCeeCCcccCCch--h-----------------
Confidence 1179999999999974333699999999999999999999 8999999999999731 0
Q ss_pred eeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCch
Q 042463 421 KLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPS 476 (490)
Q Consensus 421 ~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~ 476 (490)
+......|++|||+.|.| .||.+ ++.+.|+||+|.
T Consensus 255 -------------~~~~~~~r~~LHA~~l~f--~hp~t------~~~~~~~a~~p~ 289 (289)
T COG0564 255 -------------SAGAGLKRQALHAYKLSF--THPLT------GEELEFEAPLPE 289 (289)
T ss_pred -------------hcccCcchhhhhhceeEc--cCCCC------CCEEEEecCCCC
Confidence 000114589999999999 56766 557999999984
No 2
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=9e-55 Score=443.76 Aligned_cols=298 Identities=26% Similarity=0.385 Sum_probs=223.2
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR 182 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~ 182 (490)
+.++||++||++.++.+||+.++++|++|+|+|| | +++++++.|..||.|.++....+..
T Consensus 17 ~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VN-----------g-----~~v~~~~~v~~GD~I~i~~~~~~~~---- 76 (317)
T PRK11025 17 EAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVN-----------K-----KRIKPEYKLEAGDEVRIPPVRVAER---- 76 (317)
T ss_pred cCCchHHHHHHHhcccCCHHHHHHHHHcCCEEEC-----------C-----EEcCcccccCCCCEEEeCCCCcccc----
Confidence 3578999999998988999999999999999999 7 3567899999999999853211100
Q ss_pred ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCcee
Q 042463 183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGL 262 (490)
Q Consensus 183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGL 262 (490)
...|. .+.......+...|||||++|+|||||+||+||++.....++...+... ......+++|||||++||||
T Consensus 77 -~~~p~---~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~~~~~~~~~~~--~~~~~~~~~vhRLD~~TSGl 150 (317)
T PRK11025 77 -EEEAV---SPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRAL--RPEARFLELVHRLDRDTSGV 150 (317)
T ss_pred -ccccc---cccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCCccHHHHHHHh--ccCCCcCceeCCCCCCCceE
Confidence 00000 0000001112345999999999999999999997654333322222211 12223467999999999999
Q ss_pred EEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCC
Q 042463 263 LLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSG 342 (490)
Q Consensus 263 LLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~ 342 (490)
||||+|..+++.|+.+|+++ .|.|+|+|+|.|.+....|.|+.||.+.....+. +++..
T Consensus 151 ll~Ak~~~a~~~l~~~~~~~---------------~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~--~~~~~---- 209 (317)
T PRK11025 151 LLVAKKRSALRSLHEQLREK---------------GMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGE--RIVRV---- 209 (317)
T ss_pred EEEEcCHHHHHHHHHHHHhC---------------CccEEEEEEEeCcccCCCceEecccccCcccCCc--eEEec----
Confidence 99999999999999999986 5999999999999888789999999765332221 22211
Q ss_pred ccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceee
Q 042463 343 LEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKL 422 (490)
Q Consensus 343 ~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~ 422 (490)
...++.|.|+|++++. ..++|||+|+|.||||||||+||| ++||||+||.+||...... . +
T Consensus 210 ~~~gk~a~T~~~~l~~-~~~~sLv~~~~~TGRtHQIRvhla-~lG~PIlGD~~Yg~~~~~~---------------~--~ 270 (317)
T PRK11025 210 SQEGKPSETRFKVEER-YAFATLVRASPVTGRTHQIRVHTQ-YAGHPIAFDDRYGDREFDQ---------------Q--L 270 (317)
T ss_pred CCCCccceEEEEEeEE-cCCcEEEEEEeCCCCHHHHHHHHH-HCCCCEECCcccCCcccch---------------h--h
Confidence 1356899999999986 467899999999999999999999 8999999999999621000 0 0
Q ss_pred ecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHhh
Q 042463 423 RRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMS 486 (490)
Q Consensus 423 ~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l~ 486 (490)
. . ...+|++|||++|.|. ||.+ ++.+.|+||+|++|+.+++.|+
T Consensus 271 ~-~-----------~~~~r~~LHa~~l~f~--~P~~------~~~~~~~aplP~~~~~~l~~l~ 314 (317)
T PRK11025 271 T-G-----------TGLNRLFLHAAALKFT--HPGT------GEVMRIEAPLDEQLKRCLQKLR 314 (317)
T ss_pred h-c-----------cCCcchhhhcCcceee--CCCC------CCeEEEEcCCCHHHHHHHHHHh
Confidence 0 0 0134799999999994 6766 5569999999999999988765
No 3
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=1.1e-52 Score=425.11 Aligned_cols=294 Identities=25% Similarity=0.335 Sum_probs=220.9
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR 182 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~ 182 (490)
+.++|+++||+..++.+||+.++++|++|.|+|| |+ ..+++++.|..||.|.+.....+..
T Consensus 3 ~~g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VN-----------g~----~~~~~~~~v~~gd~I~i~~~~~~~~---- 63 (299)
T TIGR00005 3 QAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVN-----------GK----VTANPKLKVKDGDRITVRVPEEEEH---- 63 (299)
T ss_pred ccchhHHHHHHHhcccCCHHHHHHHHHCCcEEEC-----------CE----eccCcccCCCCCCEEEEecCCcccc----
Confidence 3568999999998877999999999999999999 73 2457899999999999854321100
Q ss_pred ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCC-CCCHHHHHHHHHh-ccCCCCCccccCCCcCCc
Q 042463 183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPV-HNSMDALAAAALS-YDYNEGPKLVHRLDRESS 260 (490)
Q Consensus 183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~~-~~~~~~l~~VHRLDr~TS 260 (490)
...+...++ .|+|||++|+|||||+||+||+.... ..++..++..... ......+++|||||++||
T Consensus 64 -------~~~~~~~~~-----~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TS 131 (299)
T TIGR00005 64 -------EVPPQDIPL-----DILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTS 131 (299)
T ss_pred -------cCCccCCCc-----cEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCceECCCCCCCc
Confidence 001111122 49999999999999999999976432 2334343332211 011246899999999999
Q ss_pred eeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeec
Q 042463 261 GLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQN 340 (490)
Q Consensus 261 GLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~ 340 (490)
||||||+|+++++.|+.+|.++ .|.|+|+|+|.|.++...+.|+.||.......+ ...+..
T Consensus 132 Glll~ak~~~~~~~l~~~~~~~---------------~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~~~---~~~~~~- 192 (299)
T TIGR00005 132 GLMVVAKTPLALRELQRQLKNR---------------TVTKEYVALVHGQFDSGGGTVDAPLGRVPNNRG---LMAVHP- 192 (299)
T ss_pred eEEEEEcCHHHHHHHHHHHHhC---------------CcceEEEEEEeccccCCCCEEeCceecCCCCCc---eEEEec-
Confidence 9999999999999999999886 599999999999998888999999976432222 111111
Q ss_pred CCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCce
Q 042463 341 SGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPY 420 (490)
Q Consensus 341 ~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~ 420 (490)
..+++.|.|+|+++.. ..++|+|+|+|.|||+||||+||+ ++||||+||.+||+... +.
T Consensus 193 --~~~~k~a~t~~~~l~~-~~~~slv~~~l~tGR~HQIR~hla-~lG~pI~gD~~Yg~~~~--~~--------------- 251 (299)
T TIGR00005 193 --SSEGKPAVTHFRVLER-FGNASLVECELETGRTHQIRVHLQ-YLGHPLAGDPLYGNKPV--PG--------------- 251 (299)
T ss_pred --CCCCCeeeEEEEEeEE-cCCeEEEEEEeCCCChHHHHHHHH-HCCCcEeCccccCCccc--cc---------------
Confidence 1246899999999985 457899999999999999999999 89999999999997310 00
Q ss_pred eeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHh
Q 042463 421 KLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLM 485 (490)
Q Consensus 421 ~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l 485 (490)
+.. .......|++|||++|.|. ||.+ ++.+.|+||+|++|+.+++.|
T Consensus 252 ----~~~------~~~~~~~r~~Lha~~l~f~--~p~~------~~~~~~~a~~p~~~~~~~~~~ 298 (299)
T TIGR00005 252 ----NNL------NGLLNFDRQALHAYELGFI--HPAT------GEILEFEAPLPADLVLLLEAL 298 (299)
T ss_pred ----ccc------ccccCCcchhhccCeeecc--CCCC------CCEEEEEcCChHHHHHHHHhh
Confidence 000 0000134799999999994 6766 557999999999999988754
No 4
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=1.7e-52 Score=428.53 Aligned_cols=299 Identities=22% Similarity=0.281 Sum_probs=221.5
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR 182 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~ 182 (490)
+.++||++||+..++.+||+.++++|++|+|+|| |+ ...++++.|.+||.|.+.....+..
T Consensus 15 ~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VN-----------g~----~v~~~~~~v~~gD~I~v~~~~~~~~---- 75 (325)
T PRK11180 15 QLGQRLDQALAELFPDYSRSRIKEWILDQRVLVN-----------GK----VINKPKEKVLGGEQVAIDAEIEEEA---- 75 (325)
T ss_pred cCCccHHHHHHhhccccCHHHHHHHHHCCCEEEC-----------CE----EccCCCcCcCCCCEEEEeecccccc----
Confidence 4578999999999999999999999999999999 73 1336899999999999965321110
Q ss_pred ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCC-CCCHHHHHHHHH-hccCCCCCccccCCCcCCc
Q 042463 183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPV-HNSMDALAAAAL-SYDYNEGPKLVHRLDRESS 260 (490)
Q Consensus 183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~-~~~~~~~l~~VHRLDr~TS 260 (490)
...+...+ ..|||||++|||||||+||+||++... ..++...+.... .......+++|||||++||
T Consensus 76 -------~~~~~~~~-----~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TS 143 (325)
T PRK11180 76 -------RFEPQDIP-----LDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTT 143 (325)
T ss_pred -------CCCCCCCC-----CcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCcccceeccCCCCCc
Confidence 00111112 349999999999999999999965332 233333332211 1112345789999999999
Q ss_pred eeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeec
Q 042463 261 GLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQN 340 (490)
Q Consensus 261 GLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~ 340 (490)
||||||||..++..|+++|.++ .|.|+|+|+|.|.++. +|.|+.+|..... ....+..
T Consensus 144 Glll~Ak~~~~~~~l~~~~~~~---------------~v~K~Y~A~v~G~~~~-~~~i~~~l~~~~~---~~~~~~~--- 201 (325)
T PRK11180 144 GLMVVAKTVPAQTRLVEALQKR---------------EITREYEAVAIGHMTA-GGTVDEPISRHPT---KRTHMAV--- 201 (325)
T ss_pred eeEEEECCHHHHHHHHHHHHhC---------------CcceEEEEEEecCCCC-CCEEECceecCCC---cCcEEEe---
Confidence 9999999999999999999986 5999999999999864 6889998865321 1111111
Q ss_pred CCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCce
Q 042463 341 SGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPY 420 (490)
Q Consensus 341 ~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~ 420 (490)
...++.|.|+|+++.. ..++|||+|+|.||||||||+||| ++||||+||.+||+.....
T Consensus 202 --~~~gk~a~T~~~~l~~-~~~~slv~~~~~TGRtHQIRvhla-~lG~PI~GD~~Yg~~~~~~----------------- 260 (325)
T PRK11180 202 --HPMGKPAVTHYRIMEH-FRVHTRLRLRLETGRTHQIRVHMA-HITHPLVGDQVYGGRPRPP----------------- 260 (325)
T ss_pred --CCCCcEEeEEEEEeEE-cCCeEEEEEEeCCCCHHHHHHHHH-hCCCCEeCccccCCCcccc-----------------
Confidence 1346899999999985 467899999999999999999999 8999999999999631000
Q ss_pred eeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHhhhc
Q 042463 421 KLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSY 488 (490)
Q Consensus 421 ~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l~~~ 488 (490)
.............+.|++|||++|+| .||.+ |+.+.|.||+|++|+.+++.|+..
T Consensus 261 -----~~~~~~~~~~~~~~~r~~Lha~~l~f--~hP~~------~~~~~~~a~~p~~~~~~~~~l~~~ 315 (325)
T PRK11180 261 -----KGASEEFISTLRKFDRQALHATMLRL--YHPIT------GIEMEWHAPLPQDMVELIEALRAD 315 (325)
T ss_pred -----cccchhhhhhccccchhhhhcceeEe--eCCCC------CCeEEEECCChHHHHHHHHHhhhh
Confidence 00000000011124589999999999 56766 456999999999999999887654
No 5
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=100.00 E-value=4.8e-46 Score=366.75 Aligned_cols=236 Identities=25% Similarity=0.311 Sum_probs=171.6
Q ss_pred eecCCCCcccCCCEEEEccccccccccccccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCH
Q 042463 154 RKIKTNEVMEPGARIFLPVSMVEGRISKRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSM 233 (490)
Q Consensus 154 ~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~ 233 (490)
++++.++++..||.|.+.....+. .+... ...|||||++|+|||||+||+||+.... ..
T Consensus 9 ~~~~~~~~l~~gd~i~~~~~~~~~--------------~~~~~-----~~~Iiyed~~~lvvnKPaGl~~~~~~~~--~~ 67 (246)
T cd02558 9 EPLDPDSPYRPGTFVWYYRELPDE--------------PPIPF-----EETILHQDEHLLVADKPHFLPVTPRGRY--VT 67 (246)
T ss_pred cCCCCCceecCCCEEEEeCCCCCC--------------CCCCC-----CcceEEecCCEEEEECCCCCccCCCCcc--hh
Confidence 367889999999999985321110 01111 2349999999999999999999976432 22
Q ss_pred HHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCC
Q 042463 234 DALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKE 313 (490)
Q Consensus 234 ~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~ 313 (490)
.+++..+........+++|||||++||||||||||++++..++.+|.++ .++|+|+|+|.|.++.
T Consensus 68 ~t~~~~l~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~---------------~v~K~YlA~v~G~~~~ 132 (246)
T cd02558 68 ETLLVRLRRQTGNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARR---------------EVSKTYEAVAPYVPAL 132 (246)
T ss_pred hhHHHHHHHHhCCCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcC---------------CccEEEEEEEecCCCC
Confidence 3333333222233467899999999999999999999999999999986 5999999999998864
Q ss_pred Ccc-eeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceee
Q 042463 314 KQG-IIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVG 392 (490)
Q Consensus 314 ~~g-~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvG 392 (490)
..+ .++.+|.... +. ..... .++++.|.|+|++++. ..++|+|+|+|.|||+||||+||| ++||||+|
T Consensus 133 ~~~~~~~~~i~~~~---~~-~~~~~-----~~~~~~a~T~~~~l~~-~~~~slv~~~l~TGRtHQIRvhla-~lG~PIvG 201 (246)
T cd02558 133 TFPLTVRSRIVKGR---GF-FQARE-----VEGEPNAETRIELLAR-RGGWGLYRLSPHTGKTHQLRVHMA-ALGVPILN 201 (246)
T ss_pred CCCcceeccccccC---Cc-ceeec-----cCCCCCceEEEEEEEe-cCCeEEEEEEeCCCCHHHHHHHHH-HCCCcccC
Confidence 443 3555554321 11 11111 1345789999999985 457899999999999999999999 89999999
Q ss_pred CCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEe
Q 042463 393 DYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVA 472 (490)
Q Consensus 393 D~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~a 472 (490)
|.+||...... +. +. ..+++|||++|.|. ||.| ++.+.|+|
T Consensus 202 D~~Yg~~~~~~---------------------~~--~~--------~~~~~Lha~~l~f~--hP~t------~~~~~~~~ 242 (246)
T cd02558 202 DPFYPVLLDKD---------------------PD--DF--------SRPLQLLAKELEFT--DPLT------GRPRRFES 242 (246)
T ss_pred CccCCCCCccc---------------------cc--cc--------ccCchhhhcccCcc--CCCC------CCEEEEec
Confidence 99999621000 00 00 01489999999994 6766 55799999
Q ss_pred cCc
Q 042463 473 SMP 475 (490)
Q Consensus 473 plP 475 (490)
|+|
T Consensus 243 ~~~ 245 (246)
T cd02558 243 GRS 245 (246)
T ss_pred CCC
Confidence 998
No 6
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=5.3e-46 Score=368.70 Aligned_cols=224 Identities=29% Similarity=0.343 Sum_probs=168.2
Q ss_pred eeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVN 283 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~ 283 (490)
.|||||++|||||||+||+||+..........++..+.. .....+++|||||++||||||||||+++++.|+++|+++
T Consensus 3 ~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~- 80 (257)
T PRK11112 3 EILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRD-QIGQHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQH- 80 (257)
T ss_pred cEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHH-HhCCCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhC-
Confidence 499999999999999999999763222222222222211 123357899999999999999999999999999999997
Q ss_pred cccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeecc----
Q 042463 284 KSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPM---- 359 (490)
Q Consensus 284 ~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~---- 359 (490)
.|.|+|+|+|.|.+.. ++.++.++...... ...... .....++.|.|+|++++..
T Consensus 81 --------------~v~K~Y~Alv~G~~~~-~~~i~~~l~~~~~~---~~~~~~---~~~~~~k~a~T~~~~l~~~~~~~ 139 (257)
T PRK11112 81 --------------QIQKTYHAIVRGWLME-EAVLDYPLKEELDK---IADKFA---REDKAPQPAVTHYRGLATVEMPV 139 (257)
T ss_pred --------------CcceEEEEEEEeEeCC-CCeEeeeeeecccc---cceeec---ccCCCCeEeEEEEEEEEEecccc
Confidence 5999999999998864 68898888653211 111111 1123568999999999742
Q ss_pred ------CCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccc
Q 042463 360 ------INGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKG 433 (490)
Q Consensus 360 ------~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~ 433 (490)
..+.|||+|+|.||||||||+||| ++||||+||.+||....... + ..
T Consensus 140 ~~~~~~~~~~slv~i~~~TGRtHQIRvhla-~lG~PIvGD~~Yg~~~~~~~-----------------~--~~------- 192 (257)
T PRK11112 140 ATGRYPTTRYSLVELEPKTGRKHQLRRHMA-HLRHPIIGDTKHGDLRQNRS-----------------L--AE------- 192 (257)
T ss_pred cccccCCCCeEEEEEEcCCCChHHHHHHHH-HcCCCEeCCcccCCcccchh-----------------h--hh-------
Confidence 134799999999999999999999 89999999999996310000 0 00
Q ss_pred cccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHhhh
Q 042463 434 SVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSS 487 (490)
Q Consensus 434 ~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l~~ 487 (490)
....+|++|||++|.| .||.+ ++.+.|+||+|++|+.+++.|+.
T Consensus 193 --~~~~~rl~LHA~~L~F--~hP~t------~e~~~~~a~~p~~~~~~~~~~~~ 236 (257)
T PRK11112 193 --HFGCSRLMLHASELSL--THPFT------GEPLTITAGLDETWQQLLSQFGW 236 (257)
T ss_pred --ccCCcchhHhhCccCc--cCCCC------CCEEEEEcCCCHHHHHHHHHcCC
Confidence 0013479999999999 46766 45699999999999999988764
No 7
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=7.7e-45 Score=353.32 Aligned_cols=212 Identities=29% Similarity=0.347 Sum_probs=158.5
Q ss_pred eeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVN 283 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~ 283 (490)
.|||||++|||||||+|++|++..........++..+.. .....+++|||||++||||||||+|++++..|+++|.++
T Consensus 2 ~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~- 79 (223)
T cd02563 2 EILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRD-QLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEH- 79 (223)
T ss_pred cEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHH-HcCCCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcC-
Confidence 399999999999999999999764322221222222211 123467899999999999999999999999999999997
Q ss_pred cccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeecc----
Q 042463 284 KSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPM---- 359 (490)
Q Consensus 284 ~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~---- 359 (490)
.|.|+|+|+|.|.++. +|.|+.++...... .. ...+. ....++.|.|.|+++...
T Consensus 80 --------------~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~-~~-~~~~~----~~~~~~~a~t~~~~l~~~~~~~ 138 (223)
T cd02563 80 --------------RVHKTYLAVVRGYVPE-SGTIDYPLSEELDK-LA-DKFAS----DDKAPQAATTHYRLLAVEELPV 138 (223)
T ss_pred --------------ceeEEEEEEEECccCC-CCeEEEeeeeCCCc-cc-eEEee----cCCCCceeEEEEEEeeeccccc
Confidence 5999999999999876 78999988764321 11 11111 113468899999999732
Q ss_pred ------CCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccc
Q 042463 360 ------INGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKG 433 (490)
Q Consensus 360 ------~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~ 433 (490)
..++|||+|+|.||||||||+||| ++||||+||.+||+.....+ + .
T Consensus 139 ~~~~~~~~~~slv~~~~~TGR~HQIRvhla-~lG~PIvGD~~Yg~~~~~~~-----------------~----------~ 190 (223)
T cd02563 139 VVGKYPTSRYSLVELTPHTGRKHQLRRHLA-HIRHPIIGDTTHGDGRHNRF-----------------F----------R 190 (223)
T ss_pred ccccCCCCCeEEEEEEeCCCCHHHHHHHHH-HcCCCeeCCcccCCcccChh-----------------H----------H
Confidence 124799999999999999999999 89999999999996321100 0 0
Q ss_pred cccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCc
Q 042463 434 SVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMP 475 (490)
Q Consensus 434 ~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP 475 (490)
.....+|++|||++|.|+ ||.+ |+.+.|+||+|
T Consensus 191 -~~~~~~rl~Lha~~L~F~--hP~t------~~~~~~~a~~~ 223 (223)
T cd02563 191 -EHFGCHRLLLAATRLEFT--HPVT------GERLLIEAPLD 223 (223)
T ss_pred -hhcCCccceeecCeeEee--CCCC------CCeEEEEccCC
Confidence 001135799999999994 6766 55799999987
No 8
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=100.00 E-value=2.8e-44 Score=347.92 Aligned_cols=199 Identities=28% Similarity=0.398 Sum_probs=158.6
Q ss_pred eeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVN 283 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~ 283 (490)
.|||||++|+|||||+||+||++.. ..++...+. .......+++|||||++||||||||+|+++++.|+++|.++
T Consensus 3 ~ilyed~~~lvvnKP~Gl~v~~~~~-~~~l~~~l~---~~~~~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~- 77 (217)
T TIGR01621 3 EILFTHPDFLLINKHPGISVHKDDG-ETGLLQEVA---TQLGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKR- 77 (217)
T ss_pred eEEEeCCCEEEEECCCCCeECCCCC-cChHHHHHH---HhcCCCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcC-
Confidence 4999999999999999999997643 233332222 22233568999999999999999999999999999999997
Q ss_pred cccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCc
Q 042463 284 KSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGC 363 (490)
Q Consensus 284 ~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~ 363 (490)
.|.|+|+|+|.|.++..+|.|+.++.... .+. ..+.. ..++.|.|+|+++.. .++.
T Consensus 78 --------------~v~K~YlAlV~g~~~~~~~~i~~~~~~~~--~~~---~~~~~----~~~k~a~t~~~~~~~-~~~~ 133 (217)
T TIGR01621 78 --------------KIEKTYLALSSKKPKKKQGLICGDMEKSR--RGS---WKLVN----SQENPAITRFFSASA-ATGL 133 (217)
T ss_pred --------------CccEEEEEEEeccccCCCCEEeCCcccCC--CCC---EEEeC----CCCCceeEEEEEEEE-cCCe
Confidence 59999999999999888899998886431 221 11111 245889999999985 4578
Q ss_pred eEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccccccCCcchhh
Q 042463 364 SWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLH 443 (490)
Q Consensus 364 slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~~~~~~~~rl~ 443 (490)
++++|+|.|||+||||+||+ ++||||+||.+||... ...+++
T Consensus 134 slv~~~~~TGR~HQIRvhla-~lG~PIlGD~~Yg~~~-------------------------------------~~~~~~ 175 (217)
T TIGR01621 134 RLFILKPHTGKTHQLRVAMK-SLGSPILGDPLYGTTD-------------------------------------ESDRGY 175 (217)
T ss_pred EEEEEEeCCCCHHHHHHHHH-HCCCceeCCcccCCCC-------------------------------------CccCce
Confidence 99999999999999999999 8999999999999620 013689
Q ss_pred cccccccccccCCCCCCCCCCCceEEEEecCchhHHH
Q 042463 444 LHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKI 480 (490)
Q Consensus 444 LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~ 480 (490)
|||++|.|+ |+ ++.+.|+|| |++|+.
T Consensus 176 Lha~~l~f~--~~--------~~~~~~~~~-~~~~~~ 201 (217)
T TIGR01621 176 LHAFALRFD--YQ--------NEVIQWLCD-PRQFQK 201 (217)
T ss_pred eeeeEeEEE--EC--------CeEEEEEEC-cHHHHH
Confidence 999999995 32 567999999 666643
No 9
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=3.3e-44 Score=347.89 Aligned_cols=204 Identities=29% Similarity=0.405 Sum_probs=158.4
Q ss_pred eeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVN 283 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~ 283 (490)
.|||||++|+|+|||+|++|+++.... ...++...+... ...+++|||||++||||||+|+|.+++..|+++|.++
T Consensus 15 ~iiyed~~~lvvnKPaGl~~~~~~~~~-~~~sl~~~l~~~--~~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~- 90 (219)
T PRK10158 15 VILYQDEHIMVVNKPSGLLSVPGRLEE-HKDSVMTRIQRD--YPQAESVHRLDMATSGVIVVALTKAAERELKRQFRER- 90 (219)
T ss_pred CEEEeCCCEEEEECCCCCcEeCCCCCc-cchhHHHHHHHh--CCCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhC-
Confidence 399999999999999999999754221 122333332221 1357899999999999999999999999999999986
Q ss_pred cccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCc
Q 042463 284 KSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGC 363 (490)
Q Consensus 284 ~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~ 363 (490)
.|.|+|+|+|.|.+....+.++.||...... . ....+. .++++.|.|+|++++...+..
T Consensus 91 --------------~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~--~-~~~~~~----~~~gk~a~t~~~~l~~~~~~~ 149 (219)
T PRK10158 91 --------------EPKKQYVARVWGHPSPAEGLVDLPLICDWPN--R-PKQKVC----YETGKPAQTEYEVVEYAADNT 149 (219)
T ss_pred --------------CccEEEEEEEecccCCCCcEEecceecCCCC--C-ceEEec----CCCCceeeEEEEEEEEcCCCC
Confidence 5999999999999988889999998653211 1 111111 134689999999998644445
Q ss_pred eEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccccccCCcchhh
Q 042463 364 SWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLH 443 (490)
Q Consensus 364 slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~~~~~~~~rl~ 443 (490)
++|+|+|+||||||||+||+ ++||||+||.+||.... . ...+|++
T Consensus 150 sll~~~~~TGRtHQIR~hla-~lG~PIvGD~~Yg~~~~-----------------------~-----------~~~~r~~ 194 (219)
T PRK10158 150 ARVVLKPITGRSHQLRVHML-ALGHPILGDRFYASPEA-----------------------R-----------AMAPRLL 194 (219)
T ss_pred EEEEEEeCCCCHHHHHHHHH-HCCCcEECCcccCCccc-----------------------c-----------ccccchh
Confidence 89999999999999999999 89999999999996210 0 0134799
Q ss_pred cccccccccccCCCCCCCCCCCceEEEEecCc
Q 042463 444 LHCRELKSDNLFPTLSSKPDGPDLLRFVASMP 475 (490)
Q Consensus 444 LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP 475 (490)
|||++|.|. ||.+ ++.+.|.||.|
T Consensus 195 Lha~~l~f~--~P~~------~~~~~~~a~~~ 218 (219)
T PRK10158 195 LHAEMLTIT--HPAY------GNSMTFKAPAD 218 (219)
T ss_pred hhhCccCcc--CCCC------CCeEEEEeCCC
Confidence 999999995 6766 45699999876
No 10
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=100.00 E-value=1.9e-43 Score=341.27 Aligned_cols=194 Identities=26% Similarity=0.312 Sum_probs=157.0
Q ss_pred eeeeeCCeEEEEECCCCccccCCCCC-CCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLPV-HNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDV 282 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~ 282 (490)
.|||||++|||+|||+||+|+++... ..++..++.. ......+++|||||++||||||||||++++++|+++|+++
T Consensus 17 ~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~---~~~~~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~ 93 (213)
T cd02557 17 KIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKS---EYGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSR 93 (213)
T ss_pred cEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHH---HcCCCCccCccCCCCCCceEEEEECCHHHHHHHHHHHHcC
Confidence 49999999999999999999975432 3344444432 1222458899999999999999999999999999999986
Q ss_pred ccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccC-C
Q 042463 283 NKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMI-N 361 (490)
Q Consensus 283 ~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~-~ 361 (490)
.+.|+|+|+|.|.++...+.++.+|.......+. ... ....++.|.|.|+++.... .
T Consensus 94 ---------------~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~----~~~---~~~~~~~a~t~~~~~~~~~~~ 151 (213)
T cd02557 94 ---------------EVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGGL----RND---VDEKGKDARTIFKRLSYNGDL 151 (213)
T ss_pred ---------------CccEEEEEEEeCcCCCCCeEEecceeccCcCCce----eec---cCCCCceeeEEEEEEEEcCCC
Confidence 5999999999999988889999998764322221 110 1234688999999998532 2
Q ss_pred CceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccccccCCcch
Q 042463 362 GCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPL 441 (490)
Q Consensus 362 ~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~~~~~~~~r 441 (490)
+++||+|+|.|||+||||+||+ ++||||+||.+||. .+
T Consensus 152 ~~slv~v~~~TGR~HQIR~hla-~lG~PIlGD~~Yg~-----------------------------------------~~ 189 (213)
T cd02557 152 NTSVVLCKPITGRTHQIRVHLQ-YLGHPIVNDPIYNN-----------------------------------------LG 189 (213)
T ss_pred CeEEEEEEeCCCCHHHHHHHHH-HCCCCCcCccccCC-----------------------------------------cC
Confidence 6899999999999999999999 89999999999994 15
Q ss_pred hhcccccccccccCCCCCCCCCCCceEEEEecCchhH
Q 042463 442 LHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHM 478 (490)
Q Consensus 442 l~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~ 478 (490)
|+|||++|.|+ .+.|.||+|.+|
T Consensus 190 l~Lha~~l~f~--------------~~~~~~~~p~~~ 212 (213)
T cd02557 190 IYLHALRYEGP--------------DWSYETELPDWA 212 (213)
T ss_pred hhhhhccCcCc--------------cEEEEeCCCccc
Confidence 89999999993 489999999875
No 11
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=1.4e-37 Score=318.45 Aligned_cols=308 Identities=27% Similarity=0.363 Sum_probs=215.9
Q ss_pred CCCCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccc
Q 042463 101 GRQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRIS 180 (490)
Q Consensus 101 ~~~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~ 180 (490)
..+.+..+.++++.+|...++.+.+..|+.|.|++| |+ .+.....++.||.|...++..++.
T Consensus 39 ~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n-----------~~-----~~~v~~i~k~~d~l~~~vhrh~p~-- 100 (371)
T KOG1919|consen 39 GRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVN-----------GE-----QVRVSLIVKNGDVLCHTVHRHEPP-- 100 (371)
T ss_pred eeecccchHHHHHHHHhcCchHhhhhhhhcCceEEC-----------cE-----eeeeEEEeccCCEEEEeeccCCCC--
Confidence 445566779999999999999999999999999999 73 566888999999999877654431
Q ss_pred ccccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccC-CCCCCCCHHHHHHHHHhccCCCCCccccCCCcCC
Q 042463 181 KRYDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKG-HLPVHNSMDALAAAALSYDYNEGPKLVHRLDRES 259 (490)
Q Consensus 181 ~~~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~-~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~T 259 (490)
+..+...|+|||++|+|||||+|++||+ +...++++..++... .....+.+|||||+.|
T Consensus 101 -----------------~~~~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~---~~~~~~~~~hRLDr~t 160 (371)
T KOG1919|consen 101 -----------------VAYLPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAAL---HKVEGLRPCHRLDRLT 160 (371)
T ss_pred -----------------ccccccceEEecCCEEEEeCCCCCceeccCccccccchHHHHHh---ccccccccccccCccc
Confidence 1123445999999999999999999993 333556665555432 2456689999999999
Q ss_pred ceeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEE-EEEEeCCCC-CCcceeecccccccccCCcceeEEE
Q 042463 260 SGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRY-WALVIGSPK-EKQGIIHAPLSKVLLDDGKTERIIL 337 (490)
Q Consensus 260 SGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y-~AlV~G~~~-~~~g~i~~~l~~~~~~~g~~~~~~~ 337 (490)
||||+||++.+++..++.+|+.+ .+.|.| .|-|.|.++ ...-.+..++..... ..++.+
T Consensus 161 SGllvlAkt~~~~~~~~~~~r~~---------------~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~----~~~~~l 221 (371)
T KOG1919|consen 161 SGLLVLAKTKEAADKFHEVLRKR---------------TVKKEYVVARVEGPFPVVGEVEIKEPIGEEER----PLRMGL 221 (371)
T ss_pred cceEEEEechhHhHHHHHHHhcc---------------cceeEEEEEEEeccCCCCceEEeCCCcccccc----ccceEe
Confidence 99999999999999999999987 589999 799999887 334445555543221 112222
Q ss_pred eecC--CccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCC
Q 042463 338 AQNS--GLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPT 415 (490)
Q Consensus 338 ~~~~--~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~ 415 (490)
.... +...++.|+|.|++++. .+..++|+|.|+||||||||+||+ ++|+||+||.+||+ +..|.. +|+
T Consensus 222 ~~~~~~~~~~~k~a~T~~~~~~~-~~~ss~V~~~PlTGRtHQIRvHlq-~lG~PI~gD~~Y~~--~~~~~~------~P~ 291 (371)
T KOG1919|consen 222 NAVGVRDEVAAKDAKTLFKVLSY-DGGSSLVECRPLTGRTHQIRVHLQ-YLGHPIAGDPKYGN--HIVWAG------LPF 291 (371)
T ss_pred eecccccccccccceeEEEEccc-CCceEEEEeeccCCcHHHHHHHHH-HhCCCcCCCccccc--cccccc------CCC
Confidence 2111 12347999999999997 478999999999999999999999 89999999999987 445543 344
Q ss_pred CCCceeeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCc--hhHHHHHHHhh
Q 042463 416 SGKPYKLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMP--SHMKISWNLMS 486 (490)
Q Consensus 416 t~~~~~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP--~~~~~~~~~l~ 486 (490)
+|......... .+ ....+...++++.-...| ||.++. . -+.+...++.| .|+...+..|.
T Consensus 292 ~g~~~~~~~~~-~e----~~~~~~~~~~~~~~~~~~---~~~~~~--~-~~~~~~~C~~~~~~Dl~~~lha~~ 353 (371)
T KOG1919|consen 292 TGREGTAKKKS-LE----EEIQRLIDVHLLENWLGF---HPRTGP--L-IEELCQECKVPIDNDLELFLHALK 353 (371)
T ss_pred CCCCCCccccC-cc----ccccccchhhcccccccc---cccccc--c-hhhhhhhCCCCCCchHhHhhhhcc
Confidence 44432211000 00 001112223444444433 555541 0 13456667666 77776666554
No 12
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=100.00 E-value=1.4e-36 Score=285.56 Aligned_cols=164 Identities=37% Similarity=0.549 Sum_probs=127.9
Q ss_pred EEEEECCCCccccCCCCC-CCCHHHHHHH-HHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 212 ILVLNKPPKVPLKGHLPV-HNSMDALAAA-ALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~-~~~~~~ll~~-~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
|+|+|||+|++|++.... ..++..++.. .........+++|||||++||||||||+|+++++.|+++|.++
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~------- 73 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKER------- 73 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcC-------
Confidence 589999999999976432 3334433311 1112234568999999999999999999999999999999775
Q ss_pred hhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEEE
Q 042463 290 KAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELR 369 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~ 369 (490)
.+.|+|+|+|.|.++...+.++.++..... . ...... ..++++.+.|+|++++. ..++|+++|+
T Consensus 74 --------~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~---~-~~~~~~---~~~~~~~~~t~~~~l~~-~~~~s~~~~~ 137 (185)
T cd02869 74 --------KVKKTYLALVDGKPPEDEGTIDAPLGRKKR---K-KRARVV---VSEDGKPAITHYKVLER-FGNVTLVELQ 137 (185)
T ss_pred --------ceeEEEEEEEeCCCCCCccEEecccccCCc---c-CceEEE---ECCCCeEEEEEEEEEEE-cCCcEEEEEE
Confidence 599999999999999888888887764310 0 011110 12446889999999985 4578999999
Q ss_pred eccCCCchHHHHhHhhhCCceeeCCCCCch
Q 042463 370 PLTCRKHQLRVHCAEALGTPIVGDYKYGWF 399 (490)
Q Consensus 370 l~TGRtHQIR~hla~~lG~PIvGD~~YG~~ 399 (490)
|.|||+||||+||+ ++|+||+||.+||..
T Consensus 138 l~tGR~HQIR~hl~-~~G~pIvGD~~Yg~~ 166 (185)
T cd02869 138 LETGRTHQIRVHLA-SIGHPIVGDPKYGGK 166 (185)
T ss_pred eCcCCccHHHHHHH-HCCCCEeCccccCCc
Confidence 99999999999999 899999999999973
No 13
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=8.1e-36 Score=291.64 Aligned_cols=200 Identities=16% Similarity=0.168 Sum_probs=149.7
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceec-CCCCcccCCCEEEEcccccccccccccc
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKI-KTNEVMEPGARIFLPVSMVEGRISKRYD 184 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~-~~~~~l~~Gd~I~v~~~~~e~~~~~~~~ 184 (490)
+|+++||++.+ .+||+.++++|+.|+|+|| |+ ++ ++++.+..||.|.+....
T Consensus 1 ~rld~~L~~~~-~~Sr~~~~~li~~g~V~VN-----------g~-----~~~~~~~~l~~gd~I~l~~~~---------- 53 (232)
T PRK10839 1 MRLDKFISQQL-GVSRAIAGRELRANRVTVD-----------GE-----IVKNGAFKLLPEHDVAYDGNP---------- 53 (232)
T ss_pred CcHHHHHHHcC-CCCHHHHHHHHHcCeEEEC-----------CE-----EeccCCcCcCCCCEEEECCEE----------
Confidence 47999999977 6999999999999999999 73 45 488999999999884310
Q ss_pred CCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEE
Q 042463 185 TIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLL 264 (490)
Q Consensus 185 ~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLL 264 (490)
+ ...++++|+|+|||+||+||+..+.+.++..++. ......+++|||||++||||||
T Consensus 54 -------------~------~~~~~~~~lvvnKP~G~~~~~~~~~~~tl~~~l~----~~~~~~~~~v~RLD~~TSGlll 110 (232)
T PRK10839 54 -------------L------AQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLD----EPVAYKLHAAGRLDIDTTGLVL 110 (232)
T ss_pred -------------c------ccCCCCEEEEEECCCCeEecccCCCCCeEEEecc----cccccCceecCCCCCCceeEEE
Confidence 0 0113467999999999999976554443332221 1122357899999999999999
Q ss_pred EecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCcc
Q 042463 265 MGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLE 344 (490)
Q Consensus 265 lAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~ 344 (490)
||||+++++.|.++ ++ .++|+|+|++.+.+.... +.. ...+ +. .
T Consensus 111 ~ak~~~~~~~l~~~--~~---------------~i~K~Y~a~i~~~i~~~~------~~~--~~~~----~~-------~ 154 (232)
T PRK10839 111 MTDDGQWSHRITSP--RH---------------HCEKTYLVTLESPVADDT------AEQ--FAKG----VQ-------L 154 (232)
T ss_pred EecCHHHHHHHhCC--CC---------------CCCeEEEEEECCCCCHHH------HHH--HHCC----eE-------E
Confidence 99999999988862 22 499999998877664311 000 0011 11 1
Q ss_pred ccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCC
Q 042463 345 ASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDY 394 (490)
Q Consensus 345 ~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~ 394 (490)
.++.|.|+|.+++... .++++|+|+||||||||+||+ ++||||+|=.
T Consensus 155 ~g~~a~t~~~~~~~~~--~sll~~~l~tGRtHQIR~h~~-~~G~pi~gl~ 201 (232)
T PRK10839 155 HNEKDLTKPAVLEVIT--PTQVRLTISEGRYHQVKRMFA-AVGNHVVELH 201 (232)
T ss_pred CCCcccccccEEEEec--CCEEEEEEEcCcCHHHHHHHH-HcCCeEeeEE
Confidence 2567889999998532 489999999999999999999 8999999974
No 14
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.97 E-value=1.9e-31 Score=267.92 Aligned_cols=199 Identities=13% Similarity=0.171 Sum_probs=145.8
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEccccccccccccc
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKRY 183 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~~ 183 (490)
..+||++||+. .+.+||+.++++|++|+|+|| |+ ++..++.|.+||.|.|....
T Consensus 5 ~~~RL~k~La~-~g~~SRr~a~~lI~~G~V~VN-----------Gk-----~v~~~~~V~~gD~V~v~g~~--------- 58 (290)
T PRK10475 5 SSTRLNKYISE-SGICSRREADRYIEQGNVFIN-----------GK-----RATIGDQVKAGDVVKVNGQL--------- 58 (290)
T ss_pred hHHHHHHHHHh-CCCCCHHHHHHHHHCCcEEEC-----------CE-----EccCCCCcCCCCEEEECCEE---------
Confidence 45899999998 578999999999999999999 83 56789999999999995321
Q ss_pred cCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeE
Q 042463 184 DTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLL 263 (490)
Q Consensus 184 ~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLL 263 (490)
++ ...+||++|||+|||+|++|++......++..++. . ..++++|||||++|||||
T Consensus 59 --------------i~----~~~~ed~~~lvlnKP~G~~~~~~~~~~~tv~~~l~---~---~~~l~~VgRLDrdTsGLL 114 (290)
T PRK10475 59 --------------IE----PREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVN---H---SKRVFPIGRLDKDSQGLI 114 (290)
T ss_pred --------------cc----ccccCCCeEEEEECCCCCCcCCCCCCCCcHHHHhh---c---cccccccccCCCCCcceE
Confidence 00 01247889999999999999966544444433332 1 245889999999999999
Q ss_pred EEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCc
Q 042463 264 LMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGL 343 (490)
Q Consensus 264 LlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~ 343 (490)
|||+|+++++.|.++..+ ++|+|+|+|.|.+.+. .+... ..|.. +
T Consensus 115 LlT~dg~~~~~L~~p~~~-----------------i~K~Y~v~V~g~~~~~--~l~~l------~~Gv~----l------ 159 (290)
T PRK10475 115 FLTNHGDLVNKILRAGND-----------------HEKEYLVTVDKPITDE--FIRGM------GAGVP----I------ 159 (290)
T ss_pred EEecCHHHHHHhhCcCCC-----------------CCeEEEEEECCCCCHH--HHHHH------hCCcE----E------
Confidence 999999999999876543 8999999999988652 22111 12211 0
Q ss_pred cccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeC
Q 042463 344 EASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGD 393 (490)
Q Consensus 344 ~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD 393 (490)
+++......+..+ +.++++|+|.+||+||||+||+ ++|++|+-=
T Consensus 160 ~~~~~~~~~v~~~-----~~~~~~i~l~eGk~rqIRrm~~-~~G~~V~~L 203 (290)
T PRK10475 160 LGTVTKKCKVKKE-----APFVFRITLVQGLNRQIRRMCE-HFGYEVTKL 203 (290)
T ss_pred CCEEecceEEEec-----CCcEEEEEEECCcCHHHHHHHH-HcCCEEeEE
Confidence 0000011111222 1357999999999999999999 999999753
No 15
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.97 E-value=4.9e-31 Score=265.38 Aligned_cols=205 Identities=17% Similarity=0.163 Sum_probs=144.2
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCC--CEEEEccccccccccccc
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPG--ARIFLPVSMVEGRISKRY 183 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~G--d~I~v~~~~~e~~~~~~~ 183 (490)
+||++||+. ++.+||+.++++|++|+|+|| |+ ++++++.|.++ |.|.+......
T Consensus 3 ~RL~k~La~-~g~~SRr~a~~lI~~G~V~VN-----------G~-----~~~~g~~V~~~~~d~I~v~g~~~~------- 58 (289)
T PRK10700 3 EKLQKVLAR-AGHGSRREIESIIEAGRVSVD-----------GK-----IATLGDRVEVTPGLKIRIDGHLIS------- 58 (289)
T ss_pred hhHHHHHHH-CCCCCHHHHHHHHHcCCEEEC-----------CE-----eccCCCEeCCCCCeEEEECCEEee-------
Confidence 799999998 688999999999999999999 83 56789999877 55766321100
Q ss_pred cCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCC-CCCHHHHHHHHHhccCCCCCccccCCCcCCcee
Q 042463 184 DTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPV-HNSMDALAAAALSYDYNEGPKLVHRLDRESSGL 262 (490)
Q Consensus 184 ~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGL 262 (490)
. . . ..-||+.|+++|||+|++|++.++. ..++.+++.. .....+++|||||++||||
T Consensus 59 -----------~-~-~-----~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~----~~~~~~~~VgRLD~dTsGL 116 (289)
T PRK10700 59 -----------V-K-E-----SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPK----LRGARWIAVGRLDVNTCGL 116 (289)
T ss_pred -----------c-c-c-----ccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhh----hcCCceeEccCCCCCCceE
Confidence 0 0 0 0115567999999999999966543 3444444432 1224578999999999999
Q ss_pred EEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCC
Q 042463 263 LLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSG 342 (490)
Q Consensus 263 LLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~ 342 (490)
||||+|+++++.|.++-. .|+|+|+|+|.|.+++.. +.. | ..|. .+
T Consensus 117 LLlTndg~~~~~L~~p~~-----------------~i~K~Y~v~V~G~~~~~~--l~~-l-----~~Gv----~l----- 162 (289)
T PRK10700 117 LLFTTDGELANRLMHPSR-----------------EVEREYAVRVFGQVDDAK--LRQ-L-----SRGV----QL----- 162 (289)
T ss_pred EEEEcCHHHHHHHhCccC-----------------CCCeEEEEEEccCCCHHH--HHH-H-----HcCC----Ee-----
Confidence 999999999999987422 499999999999886532 111 1 1221 11
Q ss_pred ccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeC
Q 042463 343 LEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGD 393 (490)
Q Consensus 343 ~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD 393 (490)
+++......++.+. .....++++|+|+|||+||||+||+ ++|+||+.=
T Consensus 163 -~~~~~~~~~v~~~~-~~~~~s~l~v~L~EGk~hQIRrm~~-~lG~~V~~L 210 (289)
T PRK10700 163 -EDGPAAFKTIKFSG-GEGINQWYNVTLTEGRNREVRRLWE-AVGVQVSRL 210 (289)
T ss_pred -CCceeeeEEEEecc-CCCCceEEEEEEeCCccHHHHHHHH-HcCCEEeEE
Confidence 11111112222222 1123589999999999999999999 999999864
No 16
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.97 E-value=1.3e-30 Score=239.48 Aligned_cols=148 Identities=29% Similarity=0.372 Sum_probs=111.5
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKA 291 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~ 291 (490)
|+|+|||+|++|+++..... .++..... ......+++|||||++||||||||+|+++++.|+++ ..
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~--~~~~~~l~-~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~-~~---------- 66 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRD--PTVVVRLD-KLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP-RR---------- 66 (154)
T ss_pred CEEEECCCCCEEecCCCCCC--CcHHHhhh-cccCCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh-hc----------
Confidence 58999999999997643221 22222221 123356899999999999999999999999999998 33
Q ss_pred hhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEEEec
Q 042463 292 WNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPL 371 (490)
Q Consensus 292 ~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~l~ 371 (490)
.+.|+|+|+|.|.+++ ++.+..++.. .+....+. .++++.+.|+|++++. ..++++++|+|.
T Consensus 67 ------~v~K~Y~a~v~g~~~~-~~~~~~~~~~----~~~~~~~~------~~~~~~~~t~~~~l~~-~~~~sll~~~l~ 128 (154)
T cd02550 67 ------EIEKEYLVTVRGELDE-EGIEDLATVR----RGRLSGLV------DEGVPLAVTKVRVIGE-HGGTGRLRLTLK 128 (154)
T ss_pred ------cCcEEEEEEEEeecCc-chheeccccc----cCcceeEE------cCCCcccceEEEEEEe-cCCcEEEEEEEc
Confidence 4999999999999875 4566655543 11111111 1345789999999974 456799999999
Q ss_pred cCCCchHHHHhHhhhCCceee
Q 042463 372 TCRKHQLRVHCAEALGTPIVG 392 (490)
Q Consensus 372 TGRtHQIR~hla~~lG~PIvG 392 (490)
|||+||||+||| ++||||+.
T Consensus 129 tGR~HQIR~hla-~~G~pI~~ 148 (154)
T cd02550 129 TGRTHQIRRHCA-AVGFPVLR 148 (154)
T ss_pred CCCcHHHHHHHH-HcCCcEEe
Confidence 999999999999 89999974
No 17
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=5.5e-30 Score=249.87 Aligned_cols=206 Identities=17% Similarity=0.200 Sum_probs=148.3
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCC-CEEEEccccccccccccc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPG-ARIFLPVSMVEGRISKRY 183 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~G-d~I~v~~~~~e~~~~~~~ 183 (490)
.+||++||++ .+.+||+.++++|++|+|+|| |++ ....+..+.++ |.|.+....
T Consensus 2 ~~RL~K~La~-~G~~SRr~ae~lI~~G~V~Vn-----------G~v----~~~~~~~v~~~~~~i~v~g~~--------- 56 (248)
T COG1187 2 SMRLNKFLAE-AGVGSRREAEKLIEEGRVTVN-----------GKV----ATLGGVVVDPDDDVVEVDGKR--------- 56 (248)
T ss_pred ccchHHHHHH-cCCCCHHHHHHHHHcCCEEEC-----------CEE----eccCCeEeCCCCcEEEECCEE---------
Confidence 4899999999 899999999999999999999 753 44567777777 467773321
Q ss_pred cCCCCCCCCCCcchhhcccceeee-eCCeEEEEECCCCccccCC-CCCCCCHHHHHHHHHhccCCCCCccccCCCcCCce
Q 042463 184 DTIPSGTLNPNADEIDYLRRLVKY-RDSAILVLNKPPKVPLKGH-LPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSG 261 (490)
Q Consensus 184 ~~~p~~~~~~~~~~i~~l~~~Ily-eD~~llVvNKP~Gl~v~~~-~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSG 261 (490)
+.+ +...|+++|||.|++|+.. ..++.++.+++... .....++++|+|||+||+|
T Consensus 57 ---------------------~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~--~~~~~~~~pvGRLD~dTeG 113 (248)
T COG1187 57 ---------------------IELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPER--LPRKKRLFPVGRLDKDTEG 113 (248)
T ss_pred ---------------------eeccccceEEEEECCCCeEecccCCCCCceeeeecccc--cccccceeeccccCCCCee
Confidence 223 2334999999999999855 33455555554421 1134569999999999999
Q ss_pred eEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecC
Q 042463 262 LLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNS 341 (490)
Q Consensus 262 LLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~ 341 (490)
|||||+|++++++|.++-.+ ++|+|+|.|.|.+++.. ++.. ..|. .
T Consensus 114 LLLLTnDG~la~rL~~P~~~-----------------~~K~Y~v~v~g~~~~~~--l~~l------~~Gv----~----- 159 (248)
T COG1187 114 LLLLTNDGELAHRLMHPSSE-----------------VEKEYLVRVEGPVTEED--LEKL------RKGV----T----- 159 (248)
T ss_pred EEEEeCCHHHHHHhcCCCCC-----------------CCEEEEEEEecCCCHHH--HHHH------hCCc----E-----
Confidence 99999999999999998776 89999999999876521 1111 1111 0
Q ss_pred CccccccceeEEEEeeccCC-CceEEEEEeccCCCchHHHHhHhhhCCceeeCC
Q 042463 342 GLEASQEAMTEYRVLGPMIN-GCSWIELRPLTCRKHQLRVHCAEALGTPIVGDY 394 (490)
Q Consensus 342 ~~~~~k~a~T~~~vl~~~~~-~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~ 394 (490)
.+++....+....+..... ..+|++++|.+||+||||+||+ ++|+|++.=.
T Consensus 160 -l~d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~-a~G~~V~~L~ 211 (248)
T COG1187 160 -LDDGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFE-AVGLEVLRLK 211 (248)
T ss_pred -ecCcccccceeEEEEecCCCCceEEEEEEeCCcCHHHHHHHH-HcCCEEeEEE
Confidence 1121222222122221122 5799999999999999999999 9999998754
No 18
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.96 E-value=2.3e-29 Score=232.15 Aligned_cols=153 Identities=35% Similarity=0.483 Sum_probs=111.1
Q ss_pred eEEEEECCCCccccCCCCC-CCCHHHHH-HHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccch
Q 042463 211 AILVLNKPPKVPLKGHLPV-HNSMDALA-AAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSL 288 (490)
Q Consensus 211 ~llVvNKP~Gl~v~~~~~~-~~~~~~ll-~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~ 288 (490)
+|||||||+||+|++.... ........ ...........+++|||||++||||||||+|+++++.|+++|..+
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~------ 74 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKR------ 74 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTT------
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccC------
Confidence 5899999999999976521 12222222 222233456778999999999999999999999999999999886
Q ss_pred hhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeecc--------C
Q 042463 289 SKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPM--------I 360 (490)
Q Consensus 289 ~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~--------~ 360 (490)
.++|+|+|+|.|.+....+.++.++.............. ...+++.+.|.|+++... .
T Consensus 75 ---------~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~t~~~~l~~~~~~~~~~~~ 140 (164)
T PF00849_consen 75 ---------KVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKDP-----PGRDGKPAITRYRVLRSGSRTPSKDEN 140 (164)
T ss_dssp ---------CSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCEE-----ETTTSBTSEEEEEEEEEETT---EECC
T ss_pred ---------CCcEEEEEeEcccccccceeeeccccccccccccceeee-----ecccccccceeeeeecccccccccccc
Confidence 599999999998887889999998876322211111111 135568899999999863 3
Q ss_pred CCceEEEEEeccCCCchHHHHhH
Q 042463 361 NGCSWIELRPLTCRKHQLRVHCA 383 (490)
Q Consensus 361 ~~~slvel~l~TGRtHQIR~hla 383 (490)
.++++++|+|.|||+||||+|||
T Consensus 141 ~~~s~v~~~l~tGr~HQIR~hla 163 (164)
T PF00849_consen 141 AGCSLVECELITGRTHQIRVHLA 163 (164)
T ss_dssp SSEEEEEEEESS-STTHHHHHHH
T ss_pred CCCEEEEEEECcCCCHHHHHHhc
Confidence 56899999999999999999998
No 19
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=99.96 E-value=4.1e-29 Score=232.61 Aligned_cols=144 Identities=24% Similarity=0.296 Sum_probs=103.1
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKA 291 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~ 291 (490)
|+|+|||+||+|+++.....++..++.. +.....+++|||||++||||||||+|.++++.+.+. ++
T Consensus 2 ~ivvnKP~G~~~~~~~~~~~tl~~~l~~---~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~--------- 67 (167)
T cd02553 2 YLMLNKPAGVVCATKDPHHPTVIDLLPE---PDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSP--KK--------- 67 (167)
T ss_pred EEEEECCCCCEeCCCCCCCCcHHHHhhh---hcccCCeEEcccCCCCCEEEEEEEeCHHHHHHhhCC--cC---------
Confidence 7999999999999554334444444432 222346899999999999999999999988888763 22
Q ss_pred hhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEEEec
Q 042463 292 WNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPL 371 (490)
Q Consensus 292 ~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~l~ 371 (490)
.++|+|+|+|.|.+++... .... .+ +.. . .+.+...+.+++++. ++++|+|.
T Consensus 68 ------~i~K~Y~a~V~G~~~~~~~--~~~~------~~----~~~-~----~~~~~~~~~~~~~~~-----sll~v~l~ 119 (167)
T cd02553 68 ------HVPKTYEVTLAGPLTEDDI--EAFA------EG----VLL-H----DGYPTKPAKLEILSP-----TTVRLTIT 119 (167)
T ss_pred ------CCceEEEEEEccCCCHHHH--HHHH------CC----eEE-c----CCCEeeeeEEEEeCC-----cEEEEEEE
Confidence 4999999999998865321 1111 11 110 0 001223455666642 89999999
Q ss_pred cCCCchHHHHhHhhhCCceeeCCCCCc
Q 042463 372 TCRKHQLRVHCAEALGTPIVGDYKYGW 398 (490)
Q Consensus 372 TGRtHQIR~hla~~lG~PIvGD~~YG~ 398 (490)
|||+||||+||+ ++||||++|..++-
T Consensus 120 tGR~HQIR~hla-~lG~pI~~~~R~~~ 145 (167)
T cd02553 120 EGKYHQVKRMFA-AVGNKVVALHRIRI 145 (167)
T ss_pred eCCCHHHHHHHH-HcCCeEEEEEEEEE
Confidence 999999999999 89999999977653
No 20
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=99.95 E-value=1.4e-28 Score=229.07 Aligned_cols=141 Identities=21% Similarity=0.253 Sum_probs=105.2
Q ss_pred EEEEECCCCccccCCCCC-CCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 212 ILVLNKPPKVPLKGHLPV-HNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
++|+|||+|++|++.++. ..++.+++ ..+ ....+++|||||++||||||||+|+++++.|++ .++
T Consensus 2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l---~~~-~~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~-------- 67 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLL---PKL-GIPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSN-------- 67 (167)
T ss_pred EEEEECCCCcEECccCCCCCccHHHhh---hhh-ccCceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcC--------
Confidence 789999999999964432 23333333 222 234678999999999999999999999999975 232
Q ss_pred hhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEEEe
Q 042463 291 AWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRP 370 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~l 370 (490)
.+.|+|+|+|.|.++++. +. . ...| +.. ++++.+.|+|+++.. ..++++++|+|
T Consensus 68 -------~i~K~Y~a~V~g~~~~~~--~~----~--~~~g----v~~------~~~~~~~~~~~~~~~-~~~~sll~v~l 121 (167)
T cd02556 68 -------EIEREYAVRVFGQVTDEQ--LK----S--LKKG----VEL------EDGFAGFKSIQLEGG-EGKNSWYRVTL 121 (167)
T ss_pred -------CCCeEEEEEECccCCHHH--HH----H--HHcC----CEE------CCCcCcceEEEEEec-CCCcEEEEEEE
Confidence 499999999999886532 21 0 0111 111 235678899999874 34579999999
Q ss_pred ccCCCchHHHHhHhhhCCceeeC
Q 042463 371 LTCRKHQLRVHCAEALGTPIVGD 393 (490)
Q Consensus 371 ~TGRtHQIR~hla~~lG~PIvGD 393 (490)
.|||+||||+||+ ++||||+-=
T Consensus 122 ~tGR~HQIR~~~a-~~G~pV~~L 143 (167)
T cd02556 122 REGRNREVRRLWE-AFGLQVSRL 143 (167)
T ss_pred EeCCCHHHHHHHH-HcCCeEeEE
Confidence 9999999999999 899999864
No 21
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=99.95 E-value=5.7e-29 Score=226.59 Aligned_cols=139 Identities=27% Similarity=0.309 Sum_probs=104.2
Q ss_pred EEEEECCCCccccCCCCC-CCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 212 ILVLNKPPKVPLKGHLPV-HNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
|+|+|||+|++|++..+. ..++..++. . ....+.+|||||++||||||||+|+++++.|+.+ ++
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~---~--~~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~--~~-------- 65 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLK---D--VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHP--RY-------- 65 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecc---c--cCCCEEECCCCCCCCeeEEEEeCCHHHHHHhhCc--cC--------
Confidence 589999999999965432 233322221 1 2346899999999999999999999999999763 22
Q ss_pred hhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEEEe
Q 042463 291 AWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRP 370 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~l 370 (490)
.+.|+|+|+|.|.+..+.. ... ..| +.. ++++.+.|+|++++. ..+.++++|+|
T Consensus 66 -------~i~K~Y~a~v~g~~~~~~~--~~~------~~~----~~~------~~~~~~~t~~~~l~~-~~~~sll~~~l 119 (146)
T cd02870 66 -------GVEKTYLVKVRGVPSEEEL--RRL------RAG----VEL------DDGKTAPAKVKVLSR-DPKNTLLEVTL 119 (146)
T ss_pred -------CCCeEEEEEECCCCCHHHH--HHH------HCC----eEe------CCceEcceEEEEecc-CCCCcEEEEEE
Confidence 4999999999998865321 110 111 111 235778999999974 34679999999
Q ss_pred ccCCCchHHHHhHhhhCCceee
Q 042463 371 LTCRKHQLRVHCAEALGTPIVG 392 (490)
Q Consensus 371 ~TGRtHQIR~hla~~lG~PIvG 392 (490)
.|||+||||+||+ ++|+||+.
T Consensus 120 ~tGR~HQIR~hla-~~G~pI~~ 140 (146)
T cd02870 120 HEGRNRQVRRMFE-AVGHPVLR 140 (146)
T ss_pred EeCCcHHHHHHHH-HcCCcCCe
Confidence 9999999999999 89999974
No 22
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=99.94 E-value=6.8e-27 Score=217.89 Aligned_cols=154 Identities=23% Similarity=0.227 Sum_probs=101.8
Q ss_pred EEEEECCCCccccCCCC--CCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 212 ILVLNKPPKVPLKGHLP--VHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~--~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
|+|+|||+|++|+++.+ ...++..++ . ...+++|||||++||||||||+|+++++.|.++..
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l----~---~~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~~~--------- 64 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYI----D---DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSF--------- 64 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHc----C---cCCeEEccCCCCCCeEEEEEEeCHHHHHHHHCCCC---------
Confidence 58999999999996543 223332222 1 24578999999999999999999999888877622
Q ss_pred hhhhhcccceeeEEEEEEeCCCCCCcce-eecccccccccCCcceeEEEeecCCccccccceeEEEEeecc-CCCceEEE
Q 042463 290 KAWNDACEAMYQRYWALVIGSPKEKQGI-IHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPM-INGCSWIE 367 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~G~~~~~~g~-i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~-~~~~slve 367 (490)
.++|+|+|+|.|.++..... +...+ ...++......+... +.+....|.|+++... ..+.|+++
T Consensus 65 --------~v~K~Y~a~v~g~~~~~~~~~l~~g~---~~~~~~~~~~~v~~~---~~~~~~~~~~~~~~~~~~~~~sll~ 130 (168)
T cd02566 65 --------KHPKTYYVQVEGVPTEDALEQLRNGV---ELGDGLTLPAKVEKV---DEPPWLWEREPPIRFRKNIPTSWIE 130 (168)
T ss_pred --------CCCEEEEEEECCcCCHHHHHHHhCCc---EECCeEecceEEEEe---cccccccccccccccccCCCccEEE
Confidence 39999999999998653210 01111 011221111111110 1112344555555531 23468999
Q ss_pred EEeccCCCchHHHHhHhhhCCceeeCCCC
Q 042463 368 LRPLTCRKHQLRVHCAEALGTPIVGDYKY 396 (490)
Q Consensus 368 l~l~TGRtHQIR~hla~~lG~PIvGD~~Y 396 (490)
|+|.|||+||||+||+ ++||||+.....
T Consensus 131 v~l~tGR~HQIR~~la-~lG~pV~~L~R~ 158 (168)
T cd02566 131 ITICEGKNRQVRRMTA-AVGFPTLRLIRV 158 (168)
T ss_pred EEEecCccHHHHHHHH-HcCCeEeEEEEE
Confidence 9999999999999999 899999987543
No 23
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.93 E-value=1e-25 Score=216.78 Aligned_cols=156 Identities=22% Similarity=0.277 Sum_probs=102.8
Q ss_pred CeEEEEECCCCccccCCCC-CCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccch
Q 042463 210 SAILVLNKPPKVPLKGHLP-VHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSL 288 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~-~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~ 288 (490)
..|+++|||.|++|+..++ ...++.+++. ..++++|||||++||||||||+|+++++.|.++ ..
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~-------~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~-~~------- 103 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP-------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP-GK------- 103 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhcc-------cCCeEEecCCCCCCeeEEEEECCHHHHHHHhCc-cc-------
Confidence 3489999999999985433 2344444432 246899999999999999999999999999987 22
Q ss_pred hhhhhhcccceeeEEEEEEeCCCCCCcceeeccccc-ccccCCcc--eeEEEeecCCccccccceeEEEEeec-cCCCce
Q 042463 289 SKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSK-VLLDDGKT--ERIILAQNSGLEASQEAMTEYRVLGP-MINGCS 364 (490)
Q Consensus 289 ~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~-~~~~~g~~--~~~~~~~~~~~~~~k~a~T~~~vl~~-~~~~~s 364 (490)
.+.|+|+|+|.|.+.+..... +.. ....++.. ..+...... ..-...+..+.. ...+.+
T Consensus 104 ---------~i~K~Y~~~v~g~~~~~~l~~---l~~Gv~i~~~~~~p~~~~~i~~~-----~~~~~~~~~~~~~~~~~~s 166 (217)
T PRK11394 104 ---------RTGKIYYVQVEGIPTQDALEA---LRNGVTLNDGPTLPAGAELVDEP-----AWLWPRNPPIRERKSIPTS 166 (217)
T ss_pred ---------CCCEEEEEEECCCCCHHHHHH---HhCCeEECCccccccEEEEeccc-----ccccccccccccccCCCce
Confidence 499999999999986533221 110 00111110 000000000 000000111110 112468
Q ss_pred EEEEEeccCCCchHHHHhHhhhCCceeeCCCCCc
Q 042463 365 WIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGW 398 (490)
Q Consensus 365 lvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~ 398 (490)
+++|+|.|||+||||+||+ ++|+||+||..|+-
T Consensus 167 ~l~I~L~eGR~hQIRrm~a-~lG~pVl~L~Ry~i 199 (217)
T PRK11394 167 WLKITLYEGRNRQVRRMTA-HVGFPTLRLIRYAM 199 (217)
T ss_pred EEEEEEeCCCCHHHHHHHH-HcCCeEeeeEEEEE
Confidence 9999999999999999999 89999999999975
No 24
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=99.92 E-value=1.4e-25 Score=210.60 Aligned_cols=142 Identities=20% Similarity=0.242 Sum_probs=97.5
Q ss_pred eEEEEECCCCccccCCCC----CCCC-HH-HHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcccc
Q 042463 211 AILVLNKPPKVPLKGHLP----VHNS-MD-ALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNK 284 (490)
Q Consensus 211 ~llVvNKP~Gl~v~~~~~----~~~~-~~-~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~ 284 (490)
.|+++|||+|++|+..++ +... .+ .....+.. ...++++|||||++||||||||+|+++++.|++++.
T Consensus 5 ~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~--~~~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~~~---- 78 (177)
T cd02555 5 VTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKG--HFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDAS---- 78 (177)
T ss_pred EEEEEECCCceEecCCCcccccccccccccchhhhhhh--cCCceeEecCCCCCCeeEEEEECCHHHHHHHhChhc----
Confidence 379999999999964431 1111 11 11111111 124688999999999999999999999999999753
Q ss_pred ccchhhhhhhcccceeeEEEEEEeCCCCCCcce--eecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCC
Q 042463 285 SKSLSKAWNDACEAMYQRYWALVIGSPKEKQGI--IHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMING 362 (490)
Q Consensus 285 ~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~--i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~ 362 (490)
.|.|+|+|+|.|.+++. +. +...+. .+|. ..+.+.+.+ .+
T Consensus 79 -------------~i~K~Y~v~v~g~~~~~-~l~~l~~g~~----~~~~-------------~~~~~~~~~-------~~ 120 (177)
T cd02555 79 -------------RLEQEYLVEVRGELTAG-GLERLNHGLT----YDGR-------------ELPPAKVSW-------QN 120 (177)
T ss_pred -------------CCCEEEEEEEcccCCHH-HHHHHhcCcc----cCCe-------------ecceEEEEE-------cC
Confidence 39999999999988652 21 111110 0111 012233322 12
Q ss_pred ceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCC
Q 042463 363 CSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYG 397 (490)
Q Consensus 363 ~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG 397 (490)
.++++++|.|||+||||+||+ ++||||+|+....
T Consensus 121 ~~~l~i~l~tGr~hQIR~~~~-~~G~pV~~L~R~~ 154 (177)
T cd02555 121 EQRLRFALKEPQPGQIRRMCE-SVGLEVVALRRIR 154 (177)
T ss_pred CCEEEEEEECCcChHHHHHHH-HcCCeEEEEEEEE
Confidence 479999999999999999999 8999999996653
No 25
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=99.90 E-value=3.9e-24 Score=190.64 Aligned_cols=109 Identities=27% Similarity=0.364 Sum_probs=85.4
Q ss_pred ccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCc
Q 042463 252 VHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGK 331 (490)
Q Consensus 252 VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~ 331 (490)
|||||++||||||||+|+++++.|.++ ++ .|.|+|+|+|.|.+++.. ++ ++ ..|
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~~--~~---------------~i~K~Y~a~v~g~~~~~~--~~-~~-----~~g- 54 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTHP--GH---------------HCEKTYLVTVEGPVTDED--LE-AL-----RKG- 54 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhCC--CC---------------CCCeEEEEEECCCCCHHH--HH-HH-----hCC-
Confidence 799999999999999999999999873 22 499999999999886532 11 11 111
Q ss_pred ceeEEEeecCCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCC
Q 042463 332 TERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYG 397 (490)
Q Consensus 332 ~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG 397 (490)
+.. ++++.+.+.|+++.. ..+.++++|+|.|||+||||+||+ ++|+||+||..+.
T Consensus 55 ---~~~------~~~~~~~~~~~~l~~-~~~~~~l~~~l~tGR~HQIR~~~~-~lG~pI~g~~R~~ 109 (128)
T TIGR00093 55 ---VQL------EDGPTKPAKLEVITE-PGFPTWLRITLSEGRNRQVRRMFA-AVGFPVLRLHRVR 109 (128)
T ss_pred ---eEE------CCcEEeeeEEEEEcc-CCCceEEEEEEeCCCCHHHHHHHH-HcCCeEeEEEEEE
Confidence 111 123556788888874 345789999999999999999999 8999999998775
No 26
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.89 E-value=3e-23 Score=192.28 Aligned_cols=136 Identities=16% Similarity=0.179 Sum_probs=97.8
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKA 291 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~ 291 (490)
|+++|||+|++|++++....++..++.. ...+++|||||++||||||||+|++++++|+++..+
T Consensus 2 y~~lnKP~G~l~s~~~~~~~tv~~~l~~------~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~~---------- 65 (164)
T cd02554 2 YIAYNKPVGIDCTLERADEDNIIDFVNP------PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNN---------- 65 (164)
T ss_pred EEEEECCCCcEeecCCCCCCcHHHHhcC------cCCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhcC----------
Confidence 7899999999999765444444444321 256899999999999999999999999999887775
Q ss_pred hhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEEEec
Q 042463 292 WNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIELRPL 371 (490)
Q Consensus 292 ~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel~l~ 371 (490)
+.|+|+|.|.|.+.+.. + . ....|.. . + .+.|....++.. +. ++++|.+.
T Consensus 66 -------~~K~Y~V~v~~~l~~~~--l----~--~l~~G~~----~------~---~~~~~~~~v~~~-~~-~~l~i~l~ 115 (164)
T cd02554 66 -------HEKEYLVTVNKPITDEF--I----E--GMSNGVV----I------L---GTVTKPCKVERL-AK-DKFRIVLT 115 (164)
T ss_pred -------CCeEEEEEECCCCCHHH--H----H--HHhCCCE----E------C---CeEEcceEEEEC-CC-CEEEEEEE
Confidence 89999999999886531 1 0 1111210 0 1 112222222221 12 45999999
Q ss_pred cCCCchHHHHhHhhhCCceeeCC
Q 042463 372 TCRKHQLRVHCAEALGTPIVGDY 394 (490)
Q Consensus 372 TGRtHQIR~hla~~lG~PIvGD~ 394 (490)
|||+||||+||+ ++|+||+-=.
T Consensus 116 eGr~~qIRrm~~-~~G~~V~~L~ 137 (164)
T cd02554 116 QGLNRQIRRMCE-ALGYRVTDLK 137 (164)
T ss_pred CCcCHHHHHHHH-HcCCEEEEEE
Confidence 999999999999 8999998653
No 27
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=98.83 E-value=7.6e-09 Score=100.75 Aligned_cols=73 Identities=26% Similarity=0.272 Sum_probs=52.2
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHh-ccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALS-YDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~-~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
+||||||+||.++.. ...+...+.. +......+.|||||.+|||||+||++..+ +|...|.++
T Consensus 2 ilvvnKP~Gi~s~~~------~~~~~~~l~~~~~~~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~-------- 65 (226)
T cd02868 2 LFAVYKPPGVHWKHV------RDTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSN-------- 65 (226)
T ss_pred EEEEEcCCCCChhHH------HHHHHHHHHHHccccceeeEccccCCCCceEEEEEeChhH--hHHHHHHhc--------
Confidence 799999999987532 2333332222 22222356789999999999999999876 688888874
Q ss_pred hhhhcccceeeEEEEEE
Q 042463 291 AWNDACEAMYQRYWALV 307 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV 307 (490)
.+.|+|++..
T Consensus 66 -------~~~K~Y~~~~ 75 (226)
T cd02868 66 -------HPTRVYTIRG 75 (226)
T ss_pred -------CCCeEEEEEE
Confidence 4789999754
No 28
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=98.69 E-value=6.8e-08 Score=74.80 Aligned_cols=69 Identities=20% Similarity=0.193 Sum_probs=56.8
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceec-CCCCcccCCCEEEEcccccccccccccc
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKI-KTNEVMEPGARIFLPVSMVEGRISKRYD 184 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~-~~~~~l~~Gd~I~v~~~~~e~~~~~~~~ 184 (490)
+++++||.+.++..|++.++++|++|.|+|| |+ .+ .+++.+.+||.|.+....
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn-----------~~-----~~~~~~~~v~~~d~i~i~~~~---------- 54 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVN-----------GK-----VVTKPSYKVKPGDVIEVDGKS---------- 54 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEEC-----------CE-----EccCCccCcCCCCEEEEcCCC----------
Confidence 4799999997678999999999999999999 73 44 789999999999884311
Q ss_pred CCCCCCCCCCcchhhcccceeeeeCCeEEEEE
Q 042463 185 TIPSGTLNPNADEIDYLRRLVKYRDSAILVLN 216 (490)
Q Consensus 185 ~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvN 216 (490)
+ +. .|+|||++++|+|
T Consensus 55 --------~---~~-----~i~~ed~~~lvv~ 70 (70)
T cd00165 55 --------I---EE-----DIVYEDKKLLVVN 70 (70)
T ss_pred --------c---cc-----ceeeccCCEEEeC
Confidence 0 00 4999999999987
No 29
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=98.26 E-value=2e-06 Score=63.11 Aligned_cols=48 Identities=15% Similarity=0.194 Sum_probs=41.8
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEE
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARI 168 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I 168 (490)
|||++||.+.....||++++++|+.|.|+|| |+ ...++++.+++||+|
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VN-----------g~----~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVN-----------GK----VVKDPSYIVKPGDVI 48 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTEEET-----------TE----EESSTTSBESTTEEE
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEEEEC-----------CE----EEcCCCCCCCCcCCC
Confidence 6899999986777789999999999999999 84 244599999999986
No 30
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=98.10 E-value=6.4e-06 Score=63.37 Aligned_cols=51 Identities=14% Similarity=0.043 Sum_probs=43.3
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceec-CCCCcccCCCEEEE
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKI-KTNEVMEPGARIFL 170 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~-~~~~~l~~Gd~I~v 170 (490)
.++||++||+......||+.++++|+.|.|+|| |+ .+ +++++|..||.|.|
T Consensus 7 ~~~rLd~~L~~~~~~~SR~~~k~li~~G~V~VN-----------g~-----~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 7 EYITLGQLLKELGIIDSGGQAKWFLQENEVLVN-----------GE-----LENRRGKKLYPGDVIEI 58 (59)
T ss_pred hHHHHHHHHHHcCCccCHHHHHHHHHcCCEEEC-----------CE-----EccCCCCCCCCCCEEEe
Confidence 358999999997222399999999999999999 74 44 78999999999987
No 31
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.60 E-value=9.8e-05 Score=62.40 Aligned_cols=56 Identities=13% Similarity=0.164 Sum_probs=46.6
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSM 174 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~ 174 (490)
+..||||+||-.---.-+|+.++++++.|+|++| | .+++++..|+.||+|.|....
T Consensus 6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vN-----------G-----~~aKpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVN-----------G-----QRAKPSKEVKVGDILTIRFGN 61 (100)
T ss_pred ccceehHHHHHHHHHhhhHHHHHHHHHCCeEEEC-----------C-----EEcccccccCCCCEEEEEeCC
Confidence 4579999997542114699999999999999999 7 478999999999999996554
No 32
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=97.56 E-value=0.00023 Score=67.33 Aligned_cols=70 Identities=16% Similarity=0.086 Sum_probs=51.7
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+++||||.|+.++ .++....+.....+....|-||-..||||+++-+.. .++...+.+
T Consensus 2 ~g~l~i~Kp~g~tS~----------~~v~~~k~~~~~kkvGH~GTLDp~A~GvLiv~~g~~--Tk~~~~~~~-------- 61 (182)
T cd02572 2 YGVINLDKPSGPSSH----------EVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRA--TRLVKSQQE-------- 61 (182)
T ss_pred CeEEEEecCCCCCHH----------HHHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECHH--hhhhHHHhC--------
Confidence 358999999999774 233333333345679999999999999999998863 455555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 62 ---------~~K~Y~a~v~ 71 (182)
T cd02572 62 ---------AGKEYVCVMR 71 (182)
T ss_pred ---------CCCEEEEEEE
Confidence 4699998775
No 33
>smart00363 S4 S4 RNA-binding domain.
Probab=97.45 E-value=0.00037 Score=51.87 Aligned_cols=51 Identities=18% Similarity=0.219 Sum_probs=43.8
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceec-CCCCcccCCCEEEEcc
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKI-KTNEVMEPGARIFLPV 172 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~-~~~~~l~~Gd~I~v~~ 172 (490)
++++.||...+...|++.+++++..|.|+|| |+ .+ .+++.+..||.|.+..
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vn-----------g~-----~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVN-----------GK-----KVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCEEEC-----------CE-----EecCCCeEeCCCCEEEEcc
Confidence 4789999986567899999999999999999 73 45 7899999999998844
No 34
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.32 E-value=0.00052 Score=66.98 Aligned_cols=70 Identities=17% Similarity=0.106 Sum_probs=52.0
Q ss_pred eEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 211 AILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 211 ~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
.+++||||.|+.++ .++....+.....++...|.||-..||||+++-.. .+.+|...+.+
T Consensus 10 G~l~i~KP~g~TS~----------dvv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~~--------- 69 (230)
T PRK00989 10 GILLVDKPQGRTSF----------SLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLF--------- 69 (230)
T ss_pred EEEEEeCCCCCCHH----------HHHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhcC---------
Confidence 58999999999774 33333334345668999999999999999999775 33455555554
Q ss_pred hhhhcccceeeEEEEEEe
Q 042463 291 AWNDACEAMYQRYWALVI 308 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 70 --------~~K~Y~~~~~ 79 (230)
T PRK00989 70 --------EDKEYAAVAH 79 (230)
T ss_pred --------CCcEEEEEEE
Confidence 5799999875
No 35
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.21 E-value=0.00094 Score=64.58 Aligned_cols=68 Identities=18% Similarity=0.143 Sum_probs=50.6
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKA 291 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~ 291 (490)
+++||||.|+-++ .++....+.....+....|-||-..||||+++-+.. .++...+.+
T Consensus 2 il~i~KP~g~tS~----------~vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~---------- 59 (210)
T cd00506 2 LFAVDKPQGPSSH----------DVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA---------- 59 (210)
T ss_pred EEEEEcCCCCCHH----------HHHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc----------
Confidence 7899999999774 333333333455688999999999999999998863 345555554
Q ss_pred hhhcccceeeEEEEEEe
Q 042463 292 WNDACEAMYQRYWALVI 308 (490)
Q Consensus 292 ~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 60 -------~~K~Y~~~~~ 69 (210)
T cd00506 60 -------ATKDYTAIGR 69 (210)
T ss_pred -------CCceEEEEEE
Confidence 5899999764
No 36
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.20 E-value=0.00085 Score=60.07 Aligned_cols=53 Identities=19% Similarity=0.221 Sum_probs=46.4
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
..+|||+||-..--.-||+.++.+|..|.|+|| |+ +++++..|.+||.|.|..
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vn-----------G~-----~~Kps~~V~~gd~l~v~~ 59 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYN-----------GQ-----RSKPSKIVELNATLTLRQ 59 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEEC-----------CE-----ECCCCCccCCCCEEEEEE
Confidence 358999998876656899999999999999999 73 589999999999999943
No 37
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=97.20 E-value=0.001 Score=64.15 Aligned_cols=69 Identities=20% Similarity=0.175 Sum_probs=51.7
Q ss_pred eEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 211 AILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 211 ~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
.+++||||.|+.++ .++....+.....+....|-||-..||||+++-+... +|...+.+
T Consensus 3 G~l~v~KP~g~tS~----------~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~~--------- 61 (209)
T TIGR00431 3 GVLLLDKPQGMTSF----------DALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLTD--------- 61 (209)
T ss_pred eEEEEECCCCCCHH----------HHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHcC---------
Confidence 58999999999764 3333333333456789999999999999999998743 56555554
Q ss_pred hhhhcccceeeEEEEEEe
Q 042463 291 AWNDACEAMYQRYWALVI 308 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 62 --------~~K~Y~~~~~ 71 (209)
T TIGR00431 62 --------LDKEYRAEIR 71 (209)
T ss_pred --------CCCeEEEEEE
Confidence 5799999764
No 38
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.17 E-value=0.0012 Score=64.95 Aligned_cols=70 Identities=17% Similarity=0.151 Sum_probs=51.9
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.++ .++....+.....+....|-||-..||||+++-... .+|...+.+
T Consensus 10 ~Gil~vdKP~G~TS~----------dvv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~-------- 69 (244)
T PRK00020 10 DGVLLLDKPVGLSSN----------HALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRA--TKISGRMLE-------- 69 (244)
T ss_pred CeEEEEecCCCCCHH----------HHHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECHH--hhhhHHhcc--------
Confidence 358999999999775 333333333455689999999999999999998873 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 70 ---------~~K~Y~a~~~ 79 (244)
T PRK00020 70 ---------ADKTYQATLQ 79 (244)
T ss_pred ---------CCcEEEEEEE
Confidence 4699999864
No 39
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.17 E-value=0.0011 Score=66.34 Aligned_cols=70 Identities=17% Similarity=0.171 Sum_probs=52.2
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.++++|||+|+.+| .++....+.....+....|-||-..||||+++-... .+|...+.+
T Consensus 2 ngil~vdKP~g~tS~----------~vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~-------- 61 (273)
T PRK04099 2 NRLFVANKPAGMSSN----------AFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK-------- 61 (273)
T ss_pred CeEEEEeCCCCCCHH----------HHHHHHHHHhCCCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc--------
Confidence 358999999999875 333333333355678999999999999999998874 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 62 ---------~~K~Y~a~~~ 71 (273)
T PRK04099 62 ---------TPKTYRATLW 71 (273)
T ss_pred ---------CCceEEEEEE
Confidence 4799999864
No 40
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.04 E-value=0.0018 Score=65.74 Aligned_cols=69 Identities=14% Similarity=0.064 Sum_probs=51.8
Q ss_pred eEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 211 AILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 211 ~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
.+++||||.|+.+| .++....+.....+....|-||-..||||+++-... .++...+.+
T Consensus 4 Gil~i~KP~G~TS~----------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~--------- 62 (294)
T PRK02484 4 GIINLKKEAGMTSH----------DAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMTE--------- 62 (294)
T ss_pred eEEEEeCCCCCCHH----------HHHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChh--hhhhHHhcc---------
Confidence 58999999999875 333333343455689999999999999999998864 345555554
Q ss_pred hhhhcccceeeEEEEEEe
Q 042463 291 AWNDACEAMYQRYWALVI 308 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 63 --------~~K~Y~a~~~ 72 (294)
T PRK02484 63 --------AGKVYEGEIT 72 (294)
T ss_pred --------CCcEEEEEEE
Confidence 4699999875
No 41
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=96.99 E-value=0.0019 Score=65.00 Aligned_cols=68 Identities=21% Similarity=0.185 Sum_probs=50.6
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKA 291 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~ 291 (490)
++++|||.|+.++ .++....+.....+....|-||-..||||+++-... .++...+.+
T Consensus 2 il~i~KP~G~tS~----------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~---------- 59 (279)
T PRK02193 2 IKLLYKPKGISSF----------KFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDED--TKLIDYLDQ---------- 59 (279)
T ss_pred EEEEECCCCCCHH----------HHHHHHHHHcCCCccccCccCCCcCeeEEEEEEChh--hhhhHHhcc----------
Confidence 6899999999875 333333333455679999999999999999998863 345555544
Q ss_pred hhhcccceeeEEEEEEe
Q 042463 292 WNDACEAMYQRYWALVI 308 (490)
Q Consensus 292 ~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 60 -------~~K~Y~a~~~ 69 (279)
T PRK02193 60 -------KDKTYIAKIK 69 (279)
T ss_pred -------CCcEEEEEEE
Confidence 5799999864
No 42
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=96.99 E-value=0.0021 Score=65.54 Aligned_cols=69 Identities=19% Similarity=0.085 Sum_probs=51.9
Q ss_pred eEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 211 AILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 211 ~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
.+|+||||.|+.+| .++....+.....+....|-||-..||||+++-.... ++...+.+
T Consensus 4 Gil~i~KP~G~TS~----------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~~--------- 62 (305)
T PRK14123 4 GILPVYKERGLTSH----------DVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVMD--------- 62 (305)
T ss_pred eEEEEeCCCCCCHH----------HHHHHHHHHhCCCccccCcCCCCcCeeEEEEEEChhh--hhHHHhcC---------
Confidence 58999999999775 3333333334556799999999999999999988743 45555554
Q ss_pred hhhhcccceeeEEEEEEe
Q 042463 291 AWNDACEAMYQRYWALVI 308 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 63 --------~~K~Y~~~~~ 72 (305)
T PRK14123 63 --------MGKAYEATVS 72 (305)
T ss_pred --------CCcEEEEEEE
Confidence 5799999864
No 43
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=96.96 E-value=0.0024 Score=64.70 Aligned_cols=70 Identities=19% Similarity=0.128 Sum_probs=52.2
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.+| .++....+.....+....|-||-..||||+++-... .++...+.+
T Consensus 2 ~Gil~i~KP~G~tS~----------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~-------- 61 (290)
T PRK00130 2 DGILNILKPPGMTSF----------DVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME-------- 61 (290)
T ss_pred CeEEEEeCCCCCCHH----------HHHHHHHHHhCCCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc--------
Confidence 358999999999775 333333333455679999999999999999998873 345555555
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 62 ---------~~K~Y~a~~~ 71 (290)
T PRK00130 62 ---------GKKTYRAEIK 71 (290)
T ss_pred ---------CCcEEEEEEE
Confidence 4799999864
No 44
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.96 E-value=0.0023 Score=65.67 Aligned_cols=70 Identities=20% Similarity=0.156 Sum_probs=52.0
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.++ .++....+.....+++..|-||-..||||+++-... .++...+.+
T Consensus 3 nGiL~idKP~G~TS~----------dvv~~vrk~l~~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~~-------- 62 (345)
T PRK14846 3 NYWLNIYKPRGISSA----------QLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLID-------- 62 (345)
T ss_pred CeEEEEeCCCCCCHH----------HHHHHHHHHhCCCcCCcCccCCCcCceEEEEEEChh--hhhhHHHhc--------
Confidence 468999999999774 333333343455689999999999999999998863 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 63 ---------~~K~Y~a~~~ 72 (345)
T PRK14846 63 ---------ARKTYIFTVK 72 (345)
T ss_pred ---------CCceEEEEEE
Confidence 4789999764
No 45
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=96.94 E-value=0.0022 Score=65.06 Aligned_cols=70 Identities=19% Similarity=0.210 Sum_probs=51.6
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+++||||.|+.++ .++....+.....+....|-||-..||||+++-... .++...+.+
T Consensus 9 ~Gil~i~KP~G~TS~----------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~a--TKl~~~l~~-------- 68 (298)
T PRK03287 9 SGLVVVDKPAGMTSH----------DVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERA--TKLLGHLTL-------- 68 (298)
T ss_pred CeEEEEeCCCCCCHH----------HHHHHHHHHhCCCCCCcCccCCCcceeEEEEEeChh--hhhhHHHhc--------
Confidence 469999999999775 333333333345688999999999999999998853 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 69 ---------~~K~Y~a~~~ 78 (298)
T PRK03287 69 ---------TDKSYTATIR 78 (298)
T ss_pred ---------CCcEEEEEEE
Confidence 4799999864
No 46
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=96.91 E-value=0.0025 Score=64.96 Aligned_cols=70 Identities=20% Similarity=0.139 Sum_probs=51.6
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.+| .++....+.....+....|-||-..||||+++-... .++...+.+
T Consensus 13 ~Gil~i~KP~G~TS~----------dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~-------- 72 (305)
T PRK05389 13 SGWLILDKPAGMTST----------EAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEA--TKTVPYVMD-------- 72 (305)
T ss_pred CeEEEEeCCCCCCHH----------HHHHHHHHHhcccccCCcccCCCCCceEEEEEEChh--hhhhHHhcc--------
Confidence 459999999999775 333333333345678999999999999999998863 355555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 73 ---------~~K~Y~a~~~ 82 (305)
T PRK05389 73 ---------GTKRYRFTVA 82 (305)
T ss_pred ---------CCcEEEEEEE
Confidence 4799999864
No 47
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=96.91 E-value=0.0029 Score=64.53 Aligned_cols=70 Identities=17% Similarity=0.167 Sum_probs=52.1
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+++||||.|+.+| .++....+.....+....|-||-..||||+++-... .++...+..
T Consensus 3 ~Gil~i~KP~G~TS~----------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~-------- 62 (308)
T PRK14124 3 HGFLVAYKPKGPTSH----------DVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN-------- 62 (308)
T ss_pred ceEEEEECCCCCCHH----------HHHHHHHHHcCCCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc--------
Confidence 358999999999775 333333344455679999999999999999998864 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 63 ---------~~K~Y~a~~~ 72 (308)
T PRK14124 63 ---------EKKVYYVKMR 72 (308)
T ss_pred ---------CCceEEEEEE
Confidence 4799999874
No 48
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=96.90 E-value=0.0023 Score=65.22 Aligned_cols=73 Identities=18% Similarity=0.135 Sum_probs=53.4
Q ss_pred eeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcccccc
Q 042463 207 YRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSK 286 (490)
Q Consensus 207 yeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k 286 (490)
|..+.+|++|||.|+.+| .++....+.....+....|-||-..||||+++-... .+|...+.+
T Consensus 19 ~~~~g~l~i~Kp~g~tS~----------~~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~~----- 81 (300)
T PRK04270 19 LIKFGVVNLDKPPGPTSH----------EVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALLE----- 81 (300)
T ss_pred hcCCCEEEEECCCCCCHH----------HHHHHHHHHhccccccCCCCCCCcCeEEEEEEEChH--hhhhHHhcc-----
Confidence 344679999999999775 233333333345678999999999999999998863 455555554
Q ss_pred chhhhhhhcccceeeEEEEEEe
Q 042463 287 SLSKAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 287 ~~~~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 82 ------------~~K~Y~~~~~ 91 (300)
T PRK04270 82 ------------SGKEYVCVMH 91 (300)
T ss_pred ------------CCcEEEEEEE
Confidence 4799998764
No 49
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.89 E-value=0.003 Score=64.36 Aligned_cols=70 Identities=19% Similarity=0.161 Sum_probs=52.4
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.+| .++....+.....+....+-||-..||||+++-... .+|...+.+
T Consensus 2 ~Gil~i~KP~G~TS~----------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~-------- 61 (304)
T PRK01550 2 NGVLLLHKPRGMTSH----------DCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLTD-------- 61 (304)
T ss_pred CeEEEEECCCCCCHH----------HHHHHHHHHcCCCCcccCCCCCCcCeeEEEEEEChh--hhhhHHhcC--------
Confidence 358999999999775 333333343455679999999999999999998864 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 62 ---------~~K~Y~a~~~ 71 (304)
T PRK01550 62 ---------EGKTYEGEVT 71 (304)
T ss_pred ---------CCcEEEEEEE
Confidence 4799999864
No 50
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=96.89 E-value=0.0015 Score=65.47 Aligned_cols=53 Identities=11% Similarity=0.132 Sum_probs=46.7
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
..+|||.+++..+ .+||+.++.+|++|.|+|| |+ ...++++.+++||.|.|..
T Consensus 190 as~RLD~vla~~~-~~SRsk~~~lI~~g~V~vN-----------~~----~v~~~s~~v~~gD~isiRG 242 (267)
T PLN00051 190 ASLRLDALASAGF-RMSRSKLVDLISSGDVRVN-----------WR----EVTKNGTTLKTGDVVSVSG 242 (267)
T ss_pred CcccHHHHHHHHh-ccCHHHHHHHHHcCcEEEC-----------CE----EcCCCCCCCCCCCEEEEee
Confidence 4589999999988 7999999999999999999 74 2457899999999999964
No 51
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=96.88 E-value=0.0028 Score=63.80 Aligned_cols=68 Identities=21% Similarity=0.212 Sum_probs=51.1
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKA 291 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~ 291 (490)
++++|||.|+.+| .++....+.....+....|-||-..||||+++-+.. .+|...+.+
T Consensus 2 il~i~KP~G~tS~----------~vv~~vr~~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~---------- 59 (277)
T cd02573 2 ILLLDKPAGLTSH----------DVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD---------- 59 (277)
T ss_pred EEEEECCCCCCHH----------HHHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC----------
Confidence 7899999999775 333333333445678999999999999999998864 346555554
Q ss_pred hhhcccceeeEEEEEEe
Q 042463 292 WNDACEAMYQRYWALVI 308 (490)
Q Consensus 292 ~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 60 -------~~K~Y~~~~~ 69 (277)
T cd02573 60 -------ADKTYRATVR 69 (277)
T ss_pred -------CCcEEEEEEE
Confidence 4799999875
No 52
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.87 E-value=0.0032 Score=64.04 Aligned_cols=70 Identities=19% Similarity=0.149 Sum_probs=52.2
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.+| .++....+.....+....+-||-..||||+++-... .++...+.+
T Consensus 16 ~Gil~i~KP~G~TS~----------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~-------- 75 (303)
T PRK01851 16 DGVLLLDKPLGLSSN----------DALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLLD-------- 75 (303)
T ss_pred CeEEEEeCCCCCCHH----------HHHHHHHHHhCcccCCCCCCCCCCCceEEEEEECHH--HhhhHHhcc--------
Confidence 469999999999775 333333333345678999999999999999998864 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 76 ---------~~K~Y~~~~~ 85 (303)
T PRK01851 76 ---------ADKTYEATLR 85 (303)
T ss_pred ---------cCeEEEEEEE
Confidence 4799999864
No 53
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=96.86 E-value=0.0032 Score=64.28 Aligned_cols=70 Identities=16% Similarity=0.177 Sum_probs=52.2
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.+| .++....+.....+....+-||-..||||+++-... .+|...+.+
T Consensus 10 ~Gil~i~KP~G~TS~----------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~~-------- 69 (312)
T PRK05033 10 NGVLLLDKPQGMSSN----------DALQKVKRLFNANKAGHTGALDPLATGMLPICLGEA--TKFSQYLLD-------- 69 (312)
T ss_pred CeEEEEeCCCCCCHH----------HHHHHHHHHhCCCCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhcC--------
Confidence 459999999999875 233333333355679999999999999999998864 345555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 70 ---------~~K~Y~a~~~ 79 (312)
T PRK05033 70 ---------SDKRYRVTAR 79 (312)
T ss_pred ---------CCcEEEEEEE
Confidence 4799999864
No 54
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.83 E-value=0.0035 Score=63.49 Aligned_cols=70 Identities=20% Similarity=0.140 Sum_probs=51.5
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.++ .++....+.....+....|-||-..||||+++-... .++...+.+
T Consensus 3 ~GiL~i~KP~G~TS~----------dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~~-------- 62 (292)
T PRK01528 3 NYWLNIYKPRGISSA----------KLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLID-------- 62 (292)
T ss_pred CEEEEEeCCCCCCHH----------HHHHHHHHHcCCCccCcCccCCCcCceEEEEEEChH--hhhhHHHhc--------
Confidence 468999999999775 333333333455689999999999999999998863 345555544
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 63 ---------~~K~Y~~~~~ 72 (292)
T PRK01528 63 ---------AKKTYIFTVK 72 (292)
T ss_pred ---------CCceEEEEEE
Confidence 4789999764
No 55
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.73 E-value=0.0041 Score=63.48 Aligned_cols=68 Identities=18% Similarity=0.168 Sum_probs=51.2
Q ss_pred EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhh
Q 042463 212 ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKA 291 (490)
Q Consensus 212 llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~ 291 (490)
+|+||||.|+.+| .++....+.....+....+-||-..||||+++-.... +|...+..
T Consensus 3 il~idKP~G~TS~----------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~aT--Kl~~~l~~---------- 60 (312)
T PRK14122 3 VYAVDKPLGLTSH----------DVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDST--KLVPFLSA---------- 60 (312)
T ss_pred EEEEECCCCCCHH----------HHHHHHHHHhCCCCCCCCCCCCCcCeeeEEEEEChhh--hhhHHhcC----------
Confidence 7999999999775 3333333434556899999999999999999988643 35555544
Q ss_pred hhhcccceeeEEEEEEe
Q 042463 292 WNDACEAMYQRYWALVI 308 (490)
Q Consensus 292 ~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 61 -------~~K~Y~a~~~ 70 (312)
T PRK14122 61 -------EDKEYLAWVS 70 (312)
T ss_pred -------CCceEEEEEE
Confidence 5899999874
No 56
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=96.68 E-value=0.0029 Score=60.83 Aligned_cols=54 Identities=11% Similarity=0.020 Sum_probs=45.5
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEccc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVS 173 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~ 173 (490)
.+|||++|.+.....||+.++++|..|.|.|| |+ ....+++.|.+||.|.|...
T Consensus 89 e~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VN-----------gk----~v~~ps~~V~~GD~I~V~~~ 142 (200)
T TIGR01017 89 ESRLDNVVYRLGFAPTRFAARQLVSHGHILVN-----------GK----KVDIPSYQVRPGDIISIKEK 142 (200)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCCEEEC-----------CE----EeCCCCCCCCCCCEEEEeeC
Confidence 47999999875545799999999999999999 74 24578999999999999643
No 57
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=96.67 E-value=0.005 Score=62.46 Aligned_cols=69 Identities=17% Similarity=0.115 Sum_probs=50.5
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.+| .++....+.....+....|-||-..||||+++-.... ++...+.
T Consensus 3 ~Gil~i~KP~G~TS~----------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~--------- 61 (295)
T PRK02755 3 FGFLNLDKPAGLTSH----------DCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLP--------- 61 (295)
T ss_pred ceEEEEeCCCCCCHH----------HHHHHHHHHhCCCccccCCCCCCcCeeEEEEEEChhh--hhHHHhC---------
Confidence 358999999999775 3333333334556799999999999999999988643 4554443
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
. .|+|.|.+.
T Consensus 62 --------~-~K~Y~a~~~ 71 (295)
T PRK02755 62 --------G-EKTYRGTIR 71 (295)
T ss_pred --------C-CcEEEEEEE
Confidence 2 589999764
No 58
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=96.64 E-value=0.0026 Score=63.45 Aligned_cols=54 Identities=13% Similarity=0.171 Sum_probs=46.3
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
..++||+.+++..+ .+||+.++++|++|+|+|| |+. ..++++.+.+||.|.+..
T Consensus 181 v~s~RLD~lls~~~-~~SRs~a~~lI~~G~V~VN-----------g~~----v~~~s~~v~~gD~IsvrG 234 (257)
T TIGR03069 181 EASLRIDAIASAGF-GLSRSKIVDQIKAGRLRLN-----------WKT----VTQPSRELKVGDRLQLRG 234 (257)
T ss_pred CccccHHHHHHhhh-hhhHHHHHHHHHCCeEEEC-----------CEE----cCCCCCcCCCCCEEEEcC
Confidence 34689999999877 6899999999999999999 742 347899999999999954
No 59
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=96.58 E-value=0.0037 Score=60.04 Aligned_cols=54 Identities=9% Similarity=-0.052 Sum_probs=46.1
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEccc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVS 173 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~ 173 (490)
.+|||+||.+.....||+.++++|+.|.|.|| |+ ....+++.|.+||.|.|...
T Consensus 88 E~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VN-----------Gk----~v~~ps~~Vk~GD~I~V~~~ 141 (201)
T CHL00113 88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVN-----------GR----IVDIPSYRCKPKDIITVKDK 141 (201)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCcEEEC-----------CE----EecCccccCCCCCEEEEccc
Confidence 47999999986656799999999999999999 74 24478999999999999643
No 60
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.44 E-value=0.0085 Score=60.86 Aligned_cols=70 Identities=23% Similarity=0.210 Sum_probs=52.1
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.+| .++....+.....+....+=||-..||||+++-... .+|...+.+
T Consensus 10 ~Gil~i~KP~G~TS~----------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~~-------- 69 (300)
T PRK04642 10 DGILLLDKPAGLSSN----------NALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLLG-------- 69 (300)
T ss_pred CeEEEEecCCCCCHH----------HHHHHHHHHhCCCcccCCCccCCcCeeeEEEEEChh--hhhhHHhcC--------
Confidence 469999999999875 333333343455678999999999999999998763 455555554
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 70 ---------~~K~Y~a~~~ 79 (300)
T PRK04642 70 ---------SAKAYDAEIV 79 (300)
T ss_pred ---------CCcEEEEEEE
Confidence 5799999873
No 61
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=96.43 E-value=0.0069 Score=62.37 Aligned_cols=71 Identities=17% Similarity=0.138 Sum_probs=52.5
Q ss_pred CCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccch
Q 042463 209 DSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSL 288 (490)
Q Consensus 209 D~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~ 288 (490)
.+.+|+||||.|+.+| .++....+.....+.+..+=||-..||||+++-... .+|...+.+
T Consensus 33 ~~G~l~i~KP~g~tS~----------~~v~~vr~~~~~kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~~------- 93 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSH----------EVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQE------- 93 (322)
T ss_pred CCCEEEEeCCCCCCHH----------HHHHHHHHHhcccccCCCCCCCCCCceEEEEEEChH--hhccHHhcc-------
Confidence 4569999999999775 233333333345678999999999999999998863 355555554
Q ss_pred hhhhhhcccceeeEEEEEEe
Q 042463 289 SKAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 289 ~~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 94 ----------~~K~Y~~~v~ 103 (322)
T TIGR00425 94 ----------APKEYVCLMR 103 (322)
T ss_pred ----------CCCEEEEEEE
Confidence 5799998774
No 62
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=96.28 E-value=0.0061 Score=59.80 Aligned_cols=51 Identities=16% Similarity=0.023 Sum_probs=43.7
Q ss_pred cHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 107 TAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 107 rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
||++||.......||+.++++|++|+|+|| |+ ...++++.+..||.|.+..
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vn-----------g~----~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVN-----------GK----KVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEEC-----------CE----EeCCCCCCCCCCCEEeccC
Confidence 689999997656789999999999999999 74 2458999999999998843
No 63
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=96.20 E-value=0.022 Score=47.02 Aligned_cols=22 Identities=14% Similarity=0.071 Sum_probs=19.5
Q ss_pred CCCCCccccCCCcCCceeEEEe
Q 042463 245 YNEGPKLVHRLDRESSGLLLMG 266 (490)
Q Consensus 245 ~~~~l~~VHRLDr~TSGLLLlA 266 (490)
....+..+|++|+.++|+++++
T Consensus 22 ~~~~i~~aG~kDk~a~t~q~v~ 43 (87)
T cd01291 22 PPKRVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred ChheEEECccCCCCeeEEEEEc
Confidence 3456889999999999999999
No 64
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=96.08 E-value=0.0099 Score=57.30 Aligned_cols=53 Identities=11% Similarity=0.021 Sum_probs=44.1
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
.+|||.+|.+.....||+.++++|..|.|.|| |+ ....+++.|.+||.|.+..
T Consensus 92 E~RLD~iL~~~g~~~SR~~arqlI~~G~V~VN-----------gk----~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 92 ESRLDNVVYRLGFAPTRRQARQLVSHGHILVN-----------GK----KVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred HHHHHHHHHHcCccCCHHHHHHHHHCCcEEEC-----------CE----EECCCCcCCCCCCEEEECC
Confidence 47899999775446799999999999999999 74 2345899999999999954
No 65
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.05 E-value=0.015 Score=58.37 Aligned_cols=69 Identities=23% Similarity=0.176 Sum_probs=51.7
Q ss_pred eEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhh
Q 042463 211 AILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSK 290 (490)
Q Consensus 211 ~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~ 290 (490)
.+|++|||.|+.+| ..+....+.....+.+..+-||-..||+|+++-. ++. ++...+.+
T Consensus 16 Gil~ldKP~G~tS~----------~~v~~vkkil~~~K~GH~GTLDP~atGvLpi~ig-~aT-Kl~~~l~~--------- 74 (271)
T COG0130 16 GVINLDKPPGPTSH----------EVVAWVKRILGVEKAGHGGTLDPLATGVLPICLG-EAT-KLVQYLLD--------- 74 (271)
T ss_pred ceEEeeCCCCCCHH----------HHHHHHHHHhCccccccccccCCcccceEEEEec-hhH-hHHHHHhh---------
Confidence 69999999999875 3333333444567889999999999999999998 443 44444444
Q ss_pred hhhhcccceeeEEEEEEe
Q 042463 291 AWNDACEAMYQRYWALVI 308 (490)
Q Consensus 291 ~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 75 --------~~K~Y~a~~~ 84 (271)
T COG0130 75 --------ADKEYVATVR 84 (271)
T ss_pred --------CCcEEEEEEE
Confidence 4799999875
No 66
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=95.54 E-value=0.014 Score=57.19 Aligned_cols=52 Identities=15% Similarity=0.105 Sum_probs=45.7
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
.+|||..++.-|+ +||..+..+|++|+|+|| .++ ..++++.+..||.|.+.+
T Consensus 180 SlRLD~vis~~~~-~SR~~a~~lIe~g~VkVN-----------~k~----v~~~s~~v~~GDliSirG 231 (257)
T COG2302 180 SLRLDVVISEGFG-LSRAKAQQLIEKGKVKVN-----------WKV----VDKASYEVQEGDLISIRG 231 (257)
T ss_pred hhhHHHHHHHHHh-hhHHHHHHHHHcCceEEe-----------eEE----eccccceeccCCEEEEec
Confidence 4899999999775 899999999999999999 642 455899999999999964
No 67
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=95.46 E-value=0.037 Score=56.58 Aligned_cols=43 Identities=19% Similarity=0.125 Sum_probs=32.3
Q ss_pred CCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEe
Q 042463 247 EGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 247 ~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~ 308 (490)
......|-||=..||||+++-... .+.++ .+.. ..|+|.+.+.
T Consensus 56 ~KiGH~GTLDPlAsGVLvvgvG~a-TK~l~-~~l~-----------------~~K~Y~~~~~ 98 (312)
T cd02867 56 LKIGHGGTLDPLATGVLVVGVGAG-TKQLQ-DYLS-----------------CSKTYEATGL 98 (312)
T ss_pred cccccccccCCccceeEEEEECcH-HHHHH-HHhc-----------------CCceEEEEEE
Confidence 468899999999999999998753 33343 3333 4799999764
No 68
>PRK11507 ribosome-associated protein; Provisional
Probab=95.00 E-value=0.063 Score=42.75 Aligned_cols=54 Identities=13% Similarity=0.141 Sum_probs=44.1
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
+-.+|.++|...--.-|=-.++.+|.+|.|+|| |++ ....+.++.+||.|.+..
T Consensus 10 e~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VN-----------Gev----e~rRgkKl~~GD~V~~~g 63 (70)
T PRK11507 10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVD-----------GAV----ETRKRCKIVAGQTVSFAG 63 (70)
T ss_pred CeEEHHHHHhhhCcccChHHHHHHHHcCceEEC-----------CEE----ecccCCCCCCCCEEEECC
Confidence 347899999885555788899999999999999 754 455688999999999943
No 69
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.47 E-value=0.064 Score=52.59 Aligned_cols=52 Identities=10% Similarity=0.011 Sum_probs=47.0
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
.|||+.+|.++--.-||+.++.+|.+|.|+|| |+ +..++++.|..++.|.+.
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vn-----------g~----~v~KP~~~V~~~~~i~v~ 53 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVN-----------GE----KVTKPSQLVDIDDEIEVK 53 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEEC-----------CE----EecCcceecCCCceEEEc
Confidence 58999999998667899999999999999999 75 578899999999999994
No 70
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=92.53 E-value=0.3 Score=39.17 Aligned_cols=55 Identities=13% Similarity=0.163 Sum_probs=43.5
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
.+..+|.++|.-.-=.-|=..++.+|.+|.|+|| |++ -...+.++..||.|.++.
T Consensus 9 ~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vN-----------Ge~----EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 9 TEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVN-----------GEV----ETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred cceEEHHHHHHHhCcccCcHHHHHHHHCCeEEEC-----------Cee----eeccCCEeecCCEEEECC
Confidence 3457899998884434677899999999999999 754 455678999999999943
No 71
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=92.10 E-value=0.22 Score=47.99 Aligned_cols=51 Identities=14% Similarity=0.081 Sum_probs=39.6
Q ss_pred cHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 107 TAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 107 rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
||+..+-+.-=..|+.+|+++|..|.|.|| |+ ++..|++.|.+||+|.|..
T Consensus 95 RLd~vVyR~GfA~T~~qARQlV~HGHI~Vn-----------Gk----~V~iPSy~V~~gdei~V~~ 145 (205)
T COG0522 95 RLDNVVYRLGFAKTRRQARQLVSHGHILVN-----------GK----RVNIPSYLVSPGDEISVRE 145 (205)
T ss_pred HHHHHHHHhcccccHHHHHHHhhcceEEEC-----------CE----EeccCcEEecCCCEEEeee
Confidence 444443332224799999999999999999 85 3667999999999999954
No 72
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=91.87 E-value=0.046 Score=42.95 Aligned_cols=53 Identities=13% Similarity=0.179 Sum_probs=34.4
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
+..+|.++|...--.-|=.+++.+|.+|.|+|| |++ ....+.++.+||.|.+.
T Consensus 6 e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VN-----------Ge~----e~rrg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 6 EYITLGQLLKLAGLVSSGGEAKALIQEGEVKVN-----------GEV----ETRRGKKLRPGDVVEID 58 (65)
T ss_dssp S---HHHHHHHHTS-SSSSTTSHHHHHHHHEET-----------TB--------SS----SSEEEEET
T ss_pred CcEEHHHHHhHcCCcccHHHHHHHHHcCceEEC-----------CEE----ccccCCcCCCCCEEEEC
Confidence 457889998885444577799999999999999 763 55678899999999983
No 73
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=87.08 E-value=0.99 Score=42.58 Aligned_cols=51 Identities=10% Similarity=-0.018 Sum_probs=41.6
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCC--EEEE
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGA--RIFL 170 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd--~I~v 170 (490)
..||+..|.+.--.-|+..++.+|..|.|+|| |+ .+.++++.|..++ .|.+
T Consensus 102 erRLd~il~r~gla~S~~~Ar~lI~hGhV~V~-----------g~----~V~~Ps~~V~~~~ed~I~~ 154 (177)
T PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVN-----------GR----RVTSPSYLVSVEEEDLIDY 154 (177)
T ss_pred HhHHHHHHHHccCcCCHHHHHHHHHcCCEEEC-----------CE----EeCCCCeECCCCCcceEEE
Confidence 46777777775556899999999999999999 75 3778999999885 5555
No 74
>PRK04313 30S ribosomal protein S4e; Validated
Probab=80.03 E-value=7.5 Score=38.36 Aligned_cols=54 Identities=11% Similarity=0.107 Sum_probs=42.7
Q ss_pred CCcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 103 QCHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
.+.++|.=||+..++. .+.+++++.+.+|.|.|| |++ +.+..+.+=--|+|.++
T Consensus 35 ~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VD-----------Gkv----r~D~~~PvGlmDVIsI~ 89 (237)
T PRK04313 35 EESIPLLVVLRDVLGYADTAREAKKIINEGKVLVD-----------GRV----RKDYKFPVGLMDVISIP 89 (237)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCcEEEC-----------CEE----EcccccCcCceeEEEEc
Confidence 3447788888888876 689999999999999999 853 55566666556999994
No 75
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=76.27 E-value=12 Score=37.77 Aligned_cols=54 Identities=11% Similarity=0.108 Sum_probs=42.3
Q ss_pred CCcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 103 QCHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
.+.++|.=||+..++. .+.+++++.+.+|.|.|| |++ +.+..+.+---|+|.++
T Consensus 36 ~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VD-----------Gkv----r~D~~~PvGlMDVIsI~ 90 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVD-----------GKP----RKDGKYPAGFMDVVEIP 90 (273)
T ss_pred ccccccHHHHHHHhhhhccHHHHHHHHhCCeEEEC-----------CEE----EccCCCCCceeEEEEEc
Confidence 3447788899988876 688899999999999999 853 55556665556999984
No 76
>PLN00036 40S ribosomal protein S4; Provisional
Probab=75.93 E-value=13 Score=37.32 Aligned_cols=54 Identities=9% Similarity=0.095 Sum_probs=42.1
Q ss_pred CCcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 103 QCHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
.+.++|.=||+..++. .+.+++++.+.+|.|+|| |++ +.+..+.+=--|+|.++
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VD-----------Gkv----r~D~~fPvG~mDVIsI~ 93 (261)
T PLN00036 39 RECLPLLLILRNRLKYALTYREVQAILMQRHVKVD-----------GKV----RTDKTYPAGFMDVISIP 93 (261)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCeEEEC-----------CEE----eccCCCCCceeEEEEEc
Confidence 3457888899998876 678899999999999999 853 45555655555999884
No 77
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=74.48 E-value=14 Score=37.03 Aligned_cols=54 Identities=7% Similarity=0.070 Sum_probs=42.2
Q ss_pred CCcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 103 QCHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
.+.++|.=||+..++. .+.+++++.+.+|.|.|| |++ +.+..+.+---|+|.++
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VD-----------Gkv----r~D~~fPvG~mDVIsI~ 93 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVD-----------GKV----RTDCTYPVGFMDVVSLT 93 (262)
T ss_pred ccccccHHHHHhhhhhhccHHHHHHHHHCCcEEEC-----------CEE----EccCCCCCceeEEEEEc
Confidence 3457788888888876 688899999999999999 853 45556666556999884
No 78
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=74.30 E-value=4.6 Score=36.76 Aligned_cols=33 Identities=9% Similarity=0.189 Sum_probs=30.2
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEec
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQME 136 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn 136 (490)
+...|+++.|+++++ +||+.++++++.|.|..+
T Consensus 100 ~~~~Rld~lLa~~L~-lSrs~l~~l~~~G~I~~~ 132 (142)
T PF06353_consen 100 PFPLRLDRLLARQLG-LSRSRLKRLIEQGLIRSD 132 (142)
T ss_pred CCCccHHHHHHHHhC-cCHHHHHHHHHCCCEEec
Confidence 346899999999996 899999999999999987
No 79
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=71.41 E-value=3.4 Score=37.85 Aligned_cols=44 Identities=23% Similarity=0.193 Sum_probs=31.5
Q ss_pred CCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEe
Q 042463 246 NEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 246 ~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~ 308 (490)
..+....|.||-..||||+++-+.. .+|...+.. ..|+|.|...
T Consensus 6 ~~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~-----------------~~K~Y~~~~~ 49 (149)
T PF01509_consen 6 IKKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN-----------------SDKEYVATIR 49 (149)
T ss_dssp BSSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT-----------------SEEEEEEEEE
T ss_pred cceeccccccCCcceEEEEEEECCc--chHHHHhhc-----------------cCCEEEEEEE
Confidence 3467899999999999999998763 235555554 5799999764
No 80
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=69.23 E-value=7.5 Score=36.20 Aligned_cols=49 Identities=10% Similarity=0.013 Sum_probs=35.6
Q ss_pred cHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCC--CEEEE
Q 042463 107 TAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPG--ARIFL 170 (490)
Q Consensus 107 rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~G--d~I~v 170 (490)
||+-.+-+.--.-|...+..+|..|.|+|| |+ .+..|++.|..| |.|.+
T Consensus 105 RL~~vv~r~g~a~s~~~ArqlI~hgHI~V~-----------~~----~V~~Ps~~V~~~~Ed~I~~ 155 (162)
T TIGR01018 105 RLQTQVFKKGLARTIHQARQLIVHGHIAVD-----------GR----RVTSPSYIVRREEEKKIDF 155 (162)
T ss_pred hHhhHhhhccCcCCHHHHHHHhhCCCeeEC-----------CE----EeccCceEecCCCCCeeee
Confidence 444443332234688999999999999999 75 367799999988 55555
No 81
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.75 E-value=7 Score=36.79 Aligned_cols=34 Identities=12% Similarity=0.165 Sum_probs=30.6
Q ss_pred CCCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEec
Q 042463 102 RQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQME 136 (490)
Q Consensus 102 ~~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn 136 (490)
.+...++++.|+++++ +|++.++++|+.|.|+.+
T Consensus 135 ~p~qlrl~~Ll~seL~-LSrS~lq~lie~g~Irgd 168 (203)
T COG4332 135 RPFQLRLDRLLASELG-LSRSELQRLIETGQIRGD 168 (203)
T ss_pred CcchhHHHHHHHHHhC-cCHHHHHHHHHcCceeec
Confidence 3456899999999996 899999999999999987
No 82
>KOG0062 consensus ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism; Translation, ribosomal structure and biogenesis]
Probab=64.12 E-value=13 Score=40.70 Aligned_cols=101 Identities=21% Similarity=0.371 Sum_probs=67.5
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCC-CcccCCCEEEEccccccccccccc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTN-EVMEPGARIFLPVSMVEGRISKRY 183 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~-~~l~~Gd~I~v~~~~~e~~~~~~~ 183 (490)
.+...+|+.+.++..+++++++++.. +=+. |. .+..+ ..|.-|+.++|-+.
T Consensus 443 ~v~~vd~~~~~~pG~~~ee~r~hl~~--~Gl~-----------g~-----la~~si~~LSGGQKsrvafA---------- 494 (582)
T KOG0062|consen 443 NVNAVDFMEKSFPGKTEEEIRRHLGS--FGLS-----------GE-----LALQSIASLSGGQKSRVAFA---------- 494 (582)
T ss_pred HhHHHHHHHHhCCCCCHHHHHHHHHh--cCCC-----------ch-----hhhccccccCCcchhHHHHH----------
Confidence 34568888998998999999999864 3333 32 12222 22444665555221
Q ss_pred cCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeE
Q 042463 184 DTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLL 263 (490)
Q Consensus 184 ~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLL 263 (490)
.+-+..+++||+|-|.+.. ...++++|..++..+.. ||+
T Consensus 495 --------------------~~~~~~PhlLVLDEPTNhL------D~dsl~AL~~Al~~F~G---------------GVv 533 (582)
T KOG0062|consen 495 --------------------ACTWNNPHLLVLDEPTNHL------DRDSLGALAKALKNFNG---------------GVV 533 (582)
T ss_pred --------------------HHhcCCCcEEEecCCCccc------cHHHHHHHHHHHHhcCC---------------cEE
Confidence 1456778899999998865 23567888877665532 999
Q ss_pred EEecCHHHHHH
Q 042463 264 LMGRTKESVSL 274 (490)
Q Consensus 264 LlAk~~~~a~~ 274 (490)
+++.|.++...
T Consensus 534 ~VSHd~~fi~~ 544 (582)
T KOG0062|consen 534 LVSHDEEFISS 544 (582)
T ss_pred EEECcHHHHhh
Confidence 99999887644
No 83
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=63.84 E-value=26 Score=34.46 Aligned_cols=49 Identities=14% Similarity=0.314 Sum_probs=32.5
Q ss_pred ccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCC--CEEEEc
Q 042463 106 VTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPG--ARIFLP 171 (490)
Q Consensus 106 ~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~G--d~I~v~ 171 (490)
.+|.-+++..+.. -.-+++++.|.+|.|+|| |+ +..++..-.| |+|.++
T Consensus 41 lPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VD-----------G~------vRkd~kfPVGlmDVisip 92 (241)
T COG1471 41 LPLLVIIRDYLKYADNAREARKILSEGKVLVD-----------GK------VRKDYKFPVGLMDVISIP 92 (241)
T ss_pred ccEEeeehhHHHhccchHHHHHHHhcCcEEEC-----------CE------EeccccCCcceEEEEEEC
Confidence 3444444443332 456799999999999999 84 3445555555 888884
No 84
>PLN00189 40S ribosomal protein S9; Provisional
Probab=63.29 E-value=4.4 Score=38.75 Aligned_cols=53 Identities=4% Similarity=-0.006 Sum_probs=41.7
Q ss_pred cccHHHHHHhcCC--------cCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 105 HVTAVSWVKYYFD--------EVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 105 ~~rl~~~L~~~~~--------~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
..++.+||.+++. .-|...+..+|..|.|+|| |+ .+..|++.|..|+.+.|..
T Consensus 100 ~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~-----------~~----~V~~Ps~~V~~~~e~~Itw 160 (194)
T PLN00189 100 ALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVG-----------KQ----IVNVPSFMVRVDSQKHIDF 160 (194)
T ss_pred hccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeEC-----------CE----EEecCcEEEecCCEEEEEE
Confidence 4556666666553 3588899999999999999 75 3677999999999888854
No 85
>PRK01777 hypothetical protein; Validated
Probab=54.56 E-value=16 Score=30.94 Aligned_cols=53 Identities=17% Similarity=0.129 Sum_probs=36.8
Q ss_pred CCCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 102 RQCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 102 ~~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
.+.+.|+.+.|.. ++ +....-+=-+..+.|-|| | +.++.++.|+.||+|.|+.
T Consensus 23 vp~GtTv~dal~~-sg-i~~~~pei~~~~~~vgI~-----------G-----k~v~~d~~L~dGDRVeIyr 75 (95)
T PRK01777 23 LQEGATVEEAIRA-SG-LLELRTDIDLAKNKVGIY-----------S-----RPAKLTDVLRDGDRVEIYR 75 (95)
T ss_pred cCCCCcHHHHHHH-cC-CCccCcccccccceEEEe-----------C-----eECCCCCcCCCCCEEEEec
Confidence 3456788888877 54 333311112346789999 8 5788999999999999953
No 86
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=50.12 E-value=13 Score=35.20 Aligned_cols=38 Identities=3% Similarity=-0.098 Sum_probs=31.5
Q ss_pred cCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEE
Q 042463 118 EVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFL 170 (490)
Q Consensus 118 ~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v 170 (490)
.-|...+..+|..|.|+|| |+ .+..|++.|..|+.=.|
T Consensus 119 A~ti~~ARqlI~HGHI~V~-----------~~----~V~~Ps~~V~~~~Ed~I 156 (181)
T PTZ00155 119 AKSIHHARVLIRQRHIRVG-----------KQ----IVDIPSFLVRVDSEKHI 156 (181)
T ss_pred cCCHHHhhhheeCCCEEEC-----------CE----EeccCceEeccCccCce
Confidence 3678899999999999999 75 36779999999865555
No 87
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=44.42 E-value=22 Score=29.17 Aligned_cols=46 Identities=17% Similarity=0.316 Sum_probs=36.6
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
+.+.++.+.+.. +| ++..++ |.|.|| | +.+..++.++.||.|.|..
T Consensus 30 ~~~~tvkd~IEs-LG-VP~tEV------~~i~vN-----------G-----~~v~~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 30 DGGATVKDVIES-LG-VPHTEV------GLILVN-----------G-----RPVDFDYRLKDGDRVAVYP 75 (81)
T ss_pred CCCCcHHHHHHH-cC-CChHHe------EEEEEC-----------C-----EECCCcccCCCCCEEEEEe
Confidence 345677777777 75 687766 789999 8 5788999999999999953
No 88
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=41.01 E-value=13 Score=36.65 Aligned_cols=22 Identities=36% Similarity=0.545 Sum_probs=19.2
Q ss_pred CCccccCCCcCCceeEEEecCH
Q 042463 248 GPKLVHRLDRESSGLLLMGRTK 269 (490)
Q Consensus 248 ~l~~VHRLDr~TSGLLLlAk~~ 269 (490)
...++||||-.|||++||.-+.
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 4689999999999999998663
No 89
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=40.41 E-value=36 Score=36.45 Aligned_cols=32 Identities=9% Similarity=0.039 Sum_probs=27.9
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEec
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQME 136 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn 136 (490)
++++.+.|.+.--..|+++++++|..|-|+||
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in 373 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKIN 373 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEEC
Confidence 46788988875456899999999999999999
No 90
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=38.62 E-value=59 Score=25.57 Aligned_cols=46 Identities=7% Similarity=0.236 Sum_probs=29.3
Q ss_pred cccHHHH---HHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEE
Q 042463 105 HVTAVSW---VKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFL 170 (490)
Q Consensus 105 ~~rl~~~---L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v 170 (490)
+.++.+. |...++.. .......-.|.|| | +.+..++.|+.||.|.+
T Consensus 25 ~~tv~~ll~~l~~~~~~~----~~~~~~~~~v~vN-----------g-----~~v~~~~~l~~gD~v~i 73 (80)
T cd00754 25 GATVGELLDALEARYPGL----LEELLARVRIAVN-----------G-----EYVRLDTPLKDGDEVAI 73 (80)
T ss_pred CCcHHHHHHHHHHHCchH----HHhhhhcEEEEEC-----------C-----eEcCCCcccCCCCEEEE
Confidence 3455544 44444432 2233344578899 7 35668899999999998
No 91
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=37.56 E-value=67 Score=34.34 Aligned_cols=32 Identities=9% Similarity=-0.014 Sum_probs=27.6
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEec
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQME 136 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn 136 (490)
+..+.+.|.+.--..|+++++++|..|-|+||
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in 373 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKIN 373 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEEC
Confidence 46889988875445899999999999999999
No 92
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=28.76 E-value=1.2e+02 Score=23.78 Aligned_cols=42 Identities=5% Similarity=0.188 Sum_probs=30.5
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEE
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFL 170 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v 170 (490)
.+.++.++|.. ++ ++. +.-.|.+| | ..+..++.++.||.|.+
T Consensus 22 ~~~tv~~ll~~-l~-~~~-------~~v~v~vN-----------g-----~iv~~~~~l~~gD~Vei 63 (70)
T PRK08364 22 KGMKVADILRA-VG-FNT-------ESAIAKVN-----------G-----KVALEDDPVKDGDYVEV 63 (70)
T ss_pred CCCcHHHHHHH-cC-CCC-------ccEEEEEC-----------C-----EECCCCcCcCCCCEEEE
Confidence 45688888877 53 332 23467788 7 35678999999999988
No 93
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=23.54 E-value=93 Score=33.02 Aligned_cols=77 Identities=18% Similarity=0.222 Sum_probs=48.8
Q ss_pred eeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcccccc
Q 042463 207 YRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSK 286 (490)
Q Consensus 207 yeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k 286 (490)
|--..+++++||++=.+ ..+.+.+...+ ..+..+..+-||=+.||+++...+.......+ +.
T Consensus 65 ~~~sgv~~i~kpa~pss-------~e~~swvk~iL---~~ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s-~~------- 126 (395)
T KOG2529|consen 65 YSRSGVINIDKPANPSS-------HEVVSWVKNIL---RVEKTGHSGTLDPEVTGCLIVCIDRATRLLKS-QQ------- 126 (395)
T ss_pred HhhcCceeccCCCCCch-------HHHHHHHHHHh---hHHHhCCCCCCCccccceEEEEeecccccccc-hh-------
Confidence 44445799999994221 12233333322 23456789999999999999998865432222 11
Q ss_pred chhhhhhhcccceeeEEEEEEeCCCC
Q 042463 287 SLSKAWNDACEAMYQRYWALVIGSPK 312 (490)
Q Consensus 287 ~~~~~~~~~~~~v~K~Y~AlV~G~~~ 312 (490)
...|+|.+++...+.
T Consensus 127 -----------s~gk~yvg~~~lt~~ 141 (395)
T KOG2529|consen 127 -----------SAGKEYVGIGKLTPE 141 (395)
T ss_pred -----------ccCcEEEEEEecCcc
Confidence 367899888877654
No 94
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=23.28 E-value=1.8e+02 Score=23.35 Aligned_cols=44 Identities=7% Similarity=0.041 Sum_probs=29.3
Q ss_pred cHHHHHHhcCCcCCHHHHHHHHHcCc--EEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 107 TAVSWVKYYFDEVQDSVIQSHFNKGL--VQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 107 rl~~~L~~~~~~~sr~~i~klI~~G~--V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
.+.++|..+++.. ...+..|. +.|| + +.+..++.|+.||.|.+.
T Consensus 30 ~l~~~L~~~~~~~-----~~~~~~~~~~~aVN-----------~-----~~~~~~~~l~dgDeVai~ 75 (81)
T PRK11130 30 ALRQHLAQKGDRW-----ALALEDGKLLAAVN-----------Q-----TLVSFDHPLTDGDEVAFF 75 (81)
T ss_pred HHHHHHHHhCccH-----HhhhcCCCEEEEEC-----------C-----EEcCCCCCCCCCCEEEEe
Confidence 4677777766543 22334554 6677 5 355678899999999983
No 95
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=20.77 E-value=91 Score=23.78 Aligned_cols=47 Identities=11% Similarity=0.182 Sum_probs=28.2
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEE
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFL 170 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v 170 (490)
..+.++.++|.. ++.-+. .+ .|-+| |++-+ +..-.++.|+.||+|.+
T Consensus 13 ~~~~tl~~lL~~-l~~~~~-~v-------av~vN-----------g~iv~-r~~~~~~~l~~gD~vei 59 (66)
T PRK05659 13 PDGESVAALLAR-EGLAGR-RV-------AVEVN-----------GEIVP-RSQHASTALREGDVVEI 59 (66)
T ss_pred CCCCCHHHHHHh-cCCCCC-eE-------EEEEC-----------CeEeC-HHHcCcccCCCCCEEEE
Confidence 345788888877 542222 11 26677 53200 11236889999999988
No 96
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=20.57 E-value=50 Score=25.48 Aligned_cols=18 Identities=22% Similarity=0.396 Sum_probs=12.3
Q ss_pred eeCCeEEEEECCCCcccc
Q 042463 207 YRDSAILVLNKPPKVPLK 224 (490)
Q Consensus 207 yeD~~llVvNKP~Gl~v~ 224 (490)
|-...+|.+|||+|-.+|
T Consensus 39 ~i~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 39 YIKYGVINLDKPSGPTSH 56 (59)
T ss_dssp HHHTEEEEEEE-SSS-HH
T ss_pred HHhCCcEEeeCCCCCCcc
Confidence 344679999999997665
Done!